Two anti-Castro Cubans were acquitted yesterday by a U.S. District Court jury of murder and conspiracy in connection with the 1976 car bombing assassination of former Chilean ambassador Orlando Letelier. It was a dramatic reversal of another jury's verdict more than two years ago convicting the two men of all charges.

The two defendants, Buillermo Novo Sampol and Alvin Ross Diaz, who were serving life terms in prison until a federal appeals court granted them a new trial, stood silently as jury foreman Catherine Nicholson delivered the verdict at 1:48 p.m. yesterday. The jury of eight women and four men had deliberated for almost 17 hours over three days before they reached a verdict.

The jury did convict Novo, 41, of two counts of making false declarations to a federal grand jury that was investigating the Letelier assassination, considered the most notorious act of international terrorism ever committed in Washington. Letelier, 44, and an associate, Ronni Karpen Moffitt, 25, were killed when a bomb exploded under Letelier's car as it rounded Sheridan Circle on Embassy Row on Sept. 21, 1976.

Novo's lawyer, Paul A. Goldgerger, sat on the edge of his seat at the defense table as Nicholson said that the jurors found his client "not guilty" of conspiracy and murder in connection with the two deaths. A companion of Navo's, who identified herself only as Maria, clasped the hand of Ross' wife, Sady, whom he married shortly after the two men were released from jail last April on $400,000 bond. U.S. District Judge Barrington D. Parker stopped a federal marshal who was going to silence the two sobbing women while the verdict was read.

After the jurors had left the sixthfloor courtroom, Ross and Novo and their lawyers embraced as the prosecutors stood nearby.Later, Ross, 48, said he plans to "put my life together, start working and try to overthrow Castro." Novo, who like Ross is a member of the Cuban nationalist movement in northern New Jersey, said, "I feel wonderful, wonderful. Justice has been done."

U.S. Attorney Charles F. C. Ruff listened to the verdict from the back of the courtroom with his head bowed and said afterward he had no comment on the jury's decision.

Assistant U.S. Attorney E. Lawrence Barcella Jr. said later, "It's a disappointment, but we accept the jury's verdict." Assistant U.S. attorneys H. Lowell Brown and Cary M. Feldman were also part of the prosecution team that had reassembled, the complicated murder case last March after the Justice Department decided not to ask the U.S. Supreme Court to review the appeals court ruling that reversed the original convictions. The appeals court said that testimony against Novo and Ross from fellow prisoners was improperly introduced as evidence at the first trail.

Reached by telephone at her home in Washington, Letelier's widow, Isabel, said, "I think justice has different ways of showing itself. My husband is not here any more. What can I say? Ronnie is not here any more."

The government's case had rested heavily at both trials on the testimony of their key witness, Michael Vernon Townley, an American-born agent for the Chilean secret police, once known as DINA. Townley told both juries that under orders from his DINA superiors, he recruited the Cubans to help him carry out the murder of Letelier, an ardent, outspoken critic of the military regime of Chile's president, Augusto Pinochet. Townley pleaded guilty in 1978 to conspiracy to murder a foreign official and is serving 3 1/2 to 10 years in prison.

Defense lawyers Goldberger and Lawrence A. Dubin attacked Townley during the trial as an accomplished liar who made a deal to cooperate with the U.S. government, after he was expelled from Chile in 1978, to protect himself and then implicated the Cubans to bolster the prosecution's case. Neither Novo nor Ross testified at either trial.

The defense theories at the two trials were sharply different. At the first trial, ending in convictions, the defense contended that the U.S. Central Intelligency Agency had orchestrated the murder of Letelier, with Townley acting as a double agent. At the retrial, the defense said that the Chilean government under Pinochet, DINA and Townley had carried out the murder plot and that Townley had detonated the high powered explosive that blew up Letelier's car.

Letelier, 44 at the time of his death, held various high-ranking positions under the coalition government of Marxist Salvador Allende, who was killed during a military coup led by Pinochet in September 1973. Letelier spent a year in a Chilean prison camp in the Straits of Magellan, was expelled from Chile and came to the United States with his family in 1975. He and Moffitt were employed at the Institute for Policy Studies, a leftist think tank on foreign and military affairs in Washington, when they were killed. Ronni Moffitt's husband, Michael, who was also in the car, survived.

The prosecution contended that the Cubans hoped to establish a government in exile in Chile and hoped to gain favor with that government by assisting in the assassination of Letelier, who had been stripped of his Chilean citizenship and declared an enemy of the country. The defense said the Cubans never got any help from Chile and were made "scapegoats" in the Letelier case in order to shield the Pinochet government from culpability in the murders.

After the jury announced the acquittal yesterday, Goldberger said the defense was unable to get the documents it needed to prove the CIA defense. "We felt this theory [at the retrial] made sense so we went for it," Goldberger said.

Asked if the two theories were inconsistent, Goldberger said, "You don't have to be consistent. You just have to win."

At the retrial, which lasted about 2 1/2 weeks, the defense also presented new evidence to the jury about a taped conversation of a telephone call that Townley made from the U.S. attorney's office to a friend in Chile during the original trial in January 1979. During that call, Townley made disparaging remarks about Judge Parker and said he would ask friends to make threatening calls to the judge.

The government vigorously objected at the retrial to the use of the tape, which had been provided to the defense by an attorney for Juan Manuel Contreras Sepulveda, the former head of DINA. Contreras and two other Chilean military men were also indicted in connection with the Letelier murder, but the Chilean courts have refused to extradite them for prosecution. Two other Cubans, also charged in the case, are fugitives.

The government said the tape was altered. Townley, in his testimony to the jury, said he made the comments about Parker to try to dissuade his friend from any notion that the telephone line was tampered with. The defense lawyers dwelled on the tape, emphasizing to the jury that it demonstrated Townley's total disrespect for the judicial system and undermined his credibility as a witness.

The defense also zeroed in on two statements Townley made about his role in the case to a Chilean military officer who was investigating the murders in 1978. In the first statement, Townley flatly denied his involvement in the assassination plot. Later, after Townley was expelled from Chile and brought to the United States, he requested a meeting with the same Chilean investigator. Townley testified that he wanted to be released from his secrecy voews as a DINA agent so he could talk about the Letelier murders. The defense, however, said that it was at that meeting that Townley got his instructions from Chile on the story he should tell U.S. investigators.

When Chile refused to extradite the three Chilean military men, the Carter administration retaliated with various economic and military sanctions. Despite protests from government prosecutors and human rights activists, the Reagan administration lifted two of the sanctions last February, saying that while justified in the aftermath of the murders, the santions were harming U.S. commercial and security interests.

Novo faces a maximum of 10 years in prison for his conviction of making false statements to the grand jury. The three years he has spent in jail since he was originally convicted in the Letelier case would be applied to any new prison term. Parker scheduled sentencing for June 26.