Yale University overspent its budget by $1.9 million during the 1979-80 academic year, but the deficit was the lowest the university has run in four years.

Janet H. Ackerman, director of the budget at Yale, said this week that Yale expects to balance its budget for fiscal year 1981 despite increased costs and inflation because the university is cutting expenditures for energy and faculty, decreasing its enrollment and making lucrative investments.

Although Harvard's Faculty of Arts and Sciences ran only a slight surplus-- $167,000--last year, the University as a whole ran a larger surplus and should "do well next year especially in comparison with other universities, including Yale," Ann S. Ramsay, director of the office of budgets at Harvard, said yesterday.

Ramsay attributed the University's surpluses in part to its decentralized budget system. While most other universities--including Yale--plan and manage finances centrally, Harvard allows its deans and other officials to participate in the budgeting process for the areas under their jurisdiction, she said.

"Because of the every-tub-on-its-own-bottom' system, you can easily find those areas or departments that need help," Ramsay said, adding that a more central system would make pinpointing financial problems more difficult.

Yale does not use the decentralized system because "we think there are some costs to doing that educationally," Ackerman said, adding that she believes the system discourages a student or professor from participating in more than one school within the university.

Ackerman cited conservation of energy and cutbacks in total expenditures for faculty salaries as two factors that lowered Yale's deficit for fiscal 1980.

She said the university reduced its faculty-salary budget by $750,000 after a review committee determined which empty faculty positions could remain unfilled. But she added that Yale, instead of reducing faculty salaries, is actually improving financial benefits for its professors.

Yale College's enrollment decreased by about 25 students last year, and the university will continue budgeting for 25 fewer undergraduates each year until enrollment drops from 5100 to 5000, Ackerman said.

She added that Yale President A. Bartlett Giamatti supports enrollment cutbacks and that the savings should provide more funds for facility maintenance in the long run.

But Ramsay said that despite maintenance deferral problems at Harvard, the University has no plans to lower enrollment figures in any school. "No other system is set up like ours--it allows planning in advance," Ramsay said.