D.C. mayoral assistant Joseph P. Yeldell and millionaire developer Dominic F. Antonelli Jr. pleaded innocent in federal court here yesterday to charges that they illegally conspired in the corrupt awarding of a $5.6 million city government lease.

After some initial disagreement between the attorneys for the two men - newly retained Edward Bennett Williams for Antonelli and Curtis R. Smothers for Yeldell - on the timing of the case, U.S. District Court Judge Gerhard A. Gesell set Sept. 18 as a trial date.

Yeldell's boss, longtime ally and political beneficiary, Mayor Walter E. Washington, is expected to run for reelection this fall, and the crucial Democratic primary is Sept. 12.

Because the trial will not begin until after the primary election, the issue of the innocence of Yeldell, the mayor's number two assistant, will probably remain unresolved throughout the campaign period.

At the same time, however, the September scheduling will allow the election to be completed before the trial itself begins.

"If it had been before the primary, the mayor, (city administrator Julian) Dugas and other city officials would have been called as witnesses," said one key supporter of Mayor Washington. "You don't want that to happen. Then, the story is no longer Joe Yeldell. It's what role the mayor and Dugas played in it."

Neither the mayor nor Dugas was mentioned in the indictment. Both appeared before the grand jury during its 18-month investigation.

The mayor granted Yeldell the special authority through which the lease with Antonelli was made. Before that authority was granted, Dugas, according to the director of the city's Department of General Services, had unsuccessfully urged that department to expedite a leasing agreement with Antonelli because it was "politically important."

Gesell allowed both Antonelli and Yeldell to remain free on their own recognizance. Preliminary motions are to be filed and heard by the end of June. Assistant U.S. Attonery Richard L. Beizer said about 35 to 40 witnesses are likely to be called in the trial, which he said would probably last about 21/2 weeks once a jury is chosen.

While the later date will probably be beneficial to the mayor, it could pose a financial hardship for Yeldell, whose lawyer had initially shown some willingness to accept a June trial date.

Yeldell, who sought financial assistance from Antonelli because of his own financial problems, is now on paid annual leave - vacation - from his job in order to prepare his defense. The leave can last no longer than mid-August.

Judge Gesell, after calling both men forward yesterday and receiving pleas of not guilty, made it clear that he was prepared to go to trial as early as June 6. Assistant U.S. Attorneys Beizer and Henry F. Schuelke said they were prepared to proceed as quickly as possible.

Smothers said on Yeldell's behalf that he would like at least 30 days to examine documents, but could possibly accept a June trial date as well. But Williams, who said he had only entered the case the day before and had some prior commitments. said he could not be ready for trial for at least two months.

Williams said he was "surprised" at Smothers willingness to accept the early trial date. "H'es changed this mind." Williams told the judge. "I wouldn't have come in and pressed this if I though the other defendant didn't agree."

After a half-hour recess called by an apparently bewildered Gesell, the two lawyers agreed to the September trial date. Informal arrangements were then made foreach to report for the fingerprinting and booking process required of all accused of felonies.

Antonelli arrived at the courthouse first yesterday, riding in a dark gray Lincoln Continintal and sitting in the back seat. A moderately tall and thin man who has coveted privacy much of his life, he was greeted by a pack of reporters and photographers as he walked the short distance to the courthouse door.

"I'd like to get through," he said softly but somewhat anxiously, as he quickly changed his path to avoid the group to whose questions he repeatedly answered, "No comment."

Yeldell arrived shortly afterward in a brown late-model Oldsmobile station wagon driven by one of his strongest supporters. Herbert Barksdale, who worked with Yeldell in the D.C. Department of Human Resources and later when Yeldell served as assistant to the mayor.

Like Antjonelli, Yeldell wore a dark pin-striped suit and a white shirt and dark tie. Also like Antonelli, he said only "no comment" when questioned by reporters.

Inside the courtroom, Yeldell sat on a front beach with his arm over the back, talking to his lawyer. Antonelli stood less than 15 feet away, his arms folded and leaned on a small wooden wall in front of the jury box looking the other way.

Later the two sat directly across from each other at a long, wooden table, each at a long, wooden table, each drumming his fingers on the table in front of a small wooden sign reading, "Defendant." They looked every way but at one another, and only during the short recess did they finally come together and talk for about five minutes.

Several members of Yeldell's family and some close aides and supporters attended the arraignment. They included his wife Gladys: brothers Thomas and David: Lillian Manson, his secretary; Carol Payne, also a DHR employe who went over the general assistant's staff with Yeldell and Barksdale. D.C. human rights director James W. Baldwin also came to the arraignment.

Ever since Yeldell's indictment was announced April 6, the mayor, who is expected to announce his reelection plans within two weeks, has tried to place within two weeks, has tried to place some distance between himself and Yeldell while at the same time not alienate many of the common supporters the two share.

The mayor initially did this by putting Yeldell on administrative leave immediately after the indictment while saying also that he still had confidence in him.

At a prayer breakfast two days ago, the mayor told more than 1,600 city employes, community representatives, churchmen and businessmen that he still considered "integrity and loyalty" to be among his own political assets. Observers translated that as meaning Washington felt he had been untouched by Yeldell's indictment. He would remain friends with Yeldell, his old ally, but not let the indictment quash his own political plans, the observers said.

The view of many political observers immediately after the indictment was that the biggest loss to the mayor from the indictment would be the absence of Yeldell as a strategist and architect of the mayor's reelection drive.

Since becoming the general assistant last April, Yeldell had been put in charge of many politically important and sensitive areas and is respected by many politicians as having the best political mind in the mayor's camp.

Yeldell is a accused in the indictment of engineering the awarding of profitable $5.6 million, 20-year city lease on a building owned by Antonell at 60 Florida Ave. NE that Antonelli had purchased shortly beforehand for $800,000. At the time, Yeldell was DHR director.

In return, the indictment alleges, Antonelli gave Yeldell several guarantees on an outstanding loan Yeldell held at an Antonelli bank, and also lent Yeldell an additional $33,000 which was disguised through a "straw man arrangement."