Gen. Fabian C. Ver was reinstated as chief of staff of the Philippine armed forces this afternoon, three hours after he and 25 other men were acquitted of conspiracy charges in the 1983 assassination of opposition leader Benigno Aquino.

Ver, 65, appeared in uniform before the desk of President Ferdinand Marcos at Malacanang Palace and submitted a letter formally requesting return to his post. He was put on leave after being accused last year by a civilian board of participation in the crime.

Marcos agreed to the reinstatement, but left open how long Ver would remain in office. In a statement, Marcos said the reinstatement would be "for such period as may be decided upon by me" and senior officers.

The issue of Ver's reinstatement is among the most sensitive between Washington and Manila. Ver, a cousin and close confidant of Marcos, has been described by the U.S. government as an obstacle to reform of the armed forces to combat a growing Communist insurgency.

Morale in the armed forces, which had long been plagued by corruption, charges of human rights violations, and factionalism, is said to have sagged since the Aquino assassination.

The acquittals drew strong protests from opposition leaders, who contend that Aquino was shot by one of several military security men who led him off a jetliner at Manila International Airport as he was returning from three years of self-imposed exile in the United States.

In Washington, the State Department said Ver's reinstatement raised the question of whether Marcos was serious in his "professed desire to initiate serious reforms" in the military. Rep. Stephen J. Solarz (D-N.Y.), chairman of the House Foreign Affairs subcommittee on Asia, called for a suspension of military aid as long as Ver remains in his position. Details on Page A23.

Corazon Aquino, widow of the slain politician, said after the verdict, "Justice is not possible so long as Mr. Marcos continues to be head of our government." She termed the killing "a heinous crime committed by a handful of Mr. Marcos' most loyal henchmen. I now appeal to the decent element of the military to help me get the facts and the truth."

Aquino, 52, later announced her decision to run against Marcos in elections set for Feb. 7. She made the announcement at a news conference shortly after Marcos signed into law a bill setting the poll date.

Former senator Salvador Laurel, who also plans to contest Marcos in the election, promised to reopen the case if he is elected. Of the verdict he said, "This is adding insult to injury. It insults the intelligence of the Filipino people."

Cardinal Jaime Sin, archbishop of Manila and senior prelate in this predominantly Roman Catholic country, said, "An historic opportunity to restore the credibility of the government and satisfy our people's aspirations for truth and justice was lost." Urging Filipinos not to be carried away by emotion, Sin also urged people to vote in the special presidential election, saying "the positive and democratic means for the expression of this judgment is at hand, mainly through the ballot."

Ver issued a statement declaring that he had always had faith that he would be cleared. "We can never erase the sadness and shame that befell us as the result of the assassination," the statement said. "But we can all hope to put the country back on the road to greatness."

All but one of the defendants were military personnel.

Marcos had long promised that Ver would be reinstated if found not guilty. But, apparently recognizing that controversy would continue to swirl around the general, he has hinted that Ver would be assigned to other duties soon as part of a military reorganization.

Ver, who was appointed by Marcos in 1965 to become his chief bodyguard, is one of the most powerful men in the Philippines and is known for his unflinching loyalty to Marcos. Before becoming military chief, Ver was director of the National Intelligence and Security Agency. He became armed forces chief four years ago. His sons also hold high rank in the military, and one son, Irwin, is acting chief of the Presidential Security Command.

The court's verdict effectively reversed the findings of a special five-member civilian board of inquiry that investigated the case. It concluded that Aquino's assassination was planned and executed by the military and that a cover-up ensued after the fact.

Four of the five members of the board issued a report naming Ver and the 25 others as "indictable" for the premeditated murders of Aquino and Rolando Galman, the man the military said shot Aquino. The board's chairman issued a separate dissenting report accusing only seven of the 25 military men and specifically absolving Ver.

The court's three judges supported the defendants' contention that Aquino was killed by Galman, identified by the military as a Communist agent. Galman was shot to death at the scene by security men.

Neither side may appeal the verdicts except on claims of legal error. Under the law against double jeopardy, none of the accused may be tried again for any crime related to the assassination.