The D.C. City Council voted yesterday to overhaul the city's personnel system, removing 44,000 employes from federal civil service rules and giving future mayors the right to choose and remove their cabinet-level department heads.

The measure will require, for the first time, that new employes hired by the city after Jan. 1, 1980, must live within the District of Columbia.

As part of the comprehensive 361-page personnel bill, the council gave pay increases to its own members and to the new mayor who will be elected next Tuesday and who take office on Jan. 2. The council increases is 17 percent, from $30,000 to $35,000, and the mayor's increase will be from $52,500 to $60,000.

The measure will go into effect if signed by outgoing Mayor Walter E. Washington and let stand by Congress.

Passage came on a unanimous voice vote in a council chamber crowded with union and city officials and municipal employes, and culminated more than [WORD ILLEGIBLE] years of deliberations.

Basically the bill transfers all D.C. workers from 12 existing job-classification and pay systems into a uniform citywide system starting Jan. 1, 1980. It provides for negotiations between city officials and labor unions to set the levels of pay and benefits, for most [WORD ILLEGIBLE] employes, which are now set chiefly by governmental action.

Enactment of a personnel system separate from the federal government was required by Congress in the D.C. Home Rule Charter, which took effect in 1975.

Prior to home rule, the District of Columbia funtioned virtually as a department of the U.S. government, with its personnel procedures and programs patterned after - and partly supervised by - the U.S. Civil Service Commission.

The present D.C. system is a hybrid. About half the city's employes are paid on the federal "general schedule" of salaries, the GS ratings so familiar in the Washington area. Whenever federal pay has gone up, the city has followed suit, usually also applying the increases to other city workers not on the GS sales.

The new bill does not entirely divorce the city from the federal civil service. It will continue to participate in U.S. retirement pension and health insurance programs.

One holdover from the civil service system is the job protection enjoyed by the current heads of city departments and agencies, who are members of the mayor's cabinet. Unlike top officials in most other cities, they cannot be removed except for cause, such as malfeasance or proved incompetence.

Joseph P. Yeldell, former head of the D.C. Department of Human Resources, had civil service status that led Mayor Washington to keep him in that job, and later in a post as general assistant to the mayor, even after it became known that he was being investigated for possible corruption.

Recently convicted with millionaire developer Dominic F. Antonelli on charges of conspiracy and bribery, Yeldell is still on unpaid leave from his city job. City officials are studying his status.

Under the new personnel bill, there is no question that future mayors will be able to remove top officials even without having a stated reason.

Current top officeholders cannot be fired outright, but they can be reassigned to other jobs in the city government and keep their present pay and benefits. Their replacements will serve only as long as the mayor wants them to stay in office.

The council also approved a separate bill yesterday requiring council confirmation of mayoral nominees to head departments and agencies.

Marion Barry, the Democratic nominee for mayor, has said he plans to use the new measure to remove or ask several top jobholders to leave their posts if he is elected.

Arthur A. Fletcher, the Republican nominee, has promised new management techniques but no mass firings. Yesterday he said he plans to recommend that Mayor Washington veto the new personnel bill, which he said destroys the city's job classification program.

George R. Harrod, D.C. personnel director, said he will study the bill to decide what recommendation to make to the mayor. But he noted that the bill's unanimous approval by the 13-member council make it obviously veto-proof.

Although bargaining for pay on citywide basis by employe unions is a new approach in the D.C. government, unions representing police and firefighters already have that right.

So far, however, it has not worked. Negotiations broke down in 1977 the first time they were undertaken, and the council - at Barry's urging - granted pay increases the same as federal and other D.C. workers got. They also were extended to city schoolteachers. This year, the council took similar action.

The unions representing police and firefighters actively supported passage of the new bill. Several other unions were generally neutral. But the American Federation of Government Employes, which claims to represent 9,000 D.C. employes, remains opposed. Donald MacIntyre, an AFGE vice president, said the union prefers to stick with the federal government pay scales, and expects to go to court to block the bill.

MacIntyre complained that the bill gives the council the ultimate power to block wage agreements, while outlawing all strikes of public employes.

Consideration of the personnel bill began early in 1977 by the council's government operations committee, headed by Arrington Dixon (D-Ward 4), now the Democratic nominee for council chairman.

The committee decided at the outset to model the new measure on personnel systems of the states and other large cities rather than on the federal government.

Although it provides for uniform job classifications and administrative regulations, the bill permits the city school system, the University of the District of Columbia and several quasi-judicial city boards to administer their own personnel programs separately from the city personnel department.

The new residency rule, requiring only future employes but not current ones to live in the District, is a compromise to meet objections from city workers who now live in the suburbs. About half of all the city's workers now live outside the city.

The mayor will be permitted to make exceptions in the residency requirement to cover workers at city installations in the suburbs, such as Lorton Reformatory in Virginia and Glenn Dale Hospital in Maryland.