The Supreme Court yesterday ended New York Times reporter M. A. Farber's five-week reprieve from jail in a case arising from his refusal to yield his confidential files to a judge trying a New Jersey physician on charges of murdering three of his hospital patients.

Acting in a closed conference on a motion filed by defendant, the court announced shortly after 5 p.m. in a one-sentence order, that it had nullified a stay of Farber's return to the Bergen County Jail in Hackensack.

"It's a very sad day in the history of freedom of the press," said James C. Gooddale, Times executive vice president and counsel. The reporter met with his lawyers last night. It was not immediately known when Farber would return to jail.

Farber was jailed for 27 days in August on a charge of civil contempt for refusing - in the absence of a prior hearing - to show the file in chambers to the judge presiding over the trial of Dr. Mario E. Jascalevich.

Under the order of the judge, William J. Arnold, Farber will remain in jail until the trial ends, which may occur soon after it resumes Tuesday, or until he yields the file, which he adamantly refuses to do.

The Times also has been penalized for civil contempt with daily fines of $5,000 totaling $130,000. Yesterday's action reinstates the daily fines.

Farber also has been sentenced to serve six months in jail for criminal contempt on completion of his term for civil contempt, and The Times faces a $100,000 additional fine.

The Times and Farber filed a petition with the justices Sept. 26 for review of a New jersey Supreme Court decision that, despite the state "shield" law for reporters, the constitutional gurantee of freedom of the press gives them no protection against a subpoena for confidential materials sought by the defense.

On Thursday, New Jersey Attorney General John J. Degnan joined Farber and The Times in urging the hight court to determine whether, in such circumstances, trial judges should balance the Sixth Amendment right to a fair trial and the First Amendment guarantee of a free press. The court has given no indication when it will decide whether to review the New Jersey tribunal's decision.

The stay was granted by Justice Potter Stewart Sept. 26, less than an hour before Farber was to return to jail after being freed to pursue his appeals.

Yesterday, however, Stewart apparently joined six of the eight other justices in voting in nullify the stay. Only Justice Thurgood Marshall dissented. Justice William J. Brennan Jr. did not participate.

In a brief opinion, Marshall wrote that The Times and Farber "have raised substantial claims" under the First Amendment. "Under the circumstances, I believe that both the criminal and civil penalties should be stayed until this court disposes of the petition for review," Marshall added.

Jascalevich, charged with three murders at a Oradell, N J., hospital in the mid-1960s, is seeking Farber files. Farber's investigation and articles on the death in 1974 caused authorities to reopen the probe, which resulted in the indictment of Jascalevich. The doctor contends be needs the files for his defense.