Rudolph G. Penner, a Republican economist at the American Enterprise Institute, was picked yesterday by a joint House-Senate search committee to become director of the Congressional Budget Office.

Penner, 46, who was chief economist for the Office of Management and Budget in the Ford administration, will succeed Alice Rivlin, who declined to stay in the job for a third four-year term. Rivlin is the only director CBO has ever had.

Some Democratic legislative committee chairmen mounted a campaign a few weeks ago to try to keep Penner from getting the job. However, he had the backing of most of the Democratic members of the House Budget Committee and solid support in the Republican-controlled Senate Budget Committee.

House Speaker Thomas J. (Tip) O'Neill and Senate president pro tem Strom Thurmond will make the appointment upon the recommendation of the two budget committees.

Penner is an eclectic economist who has expressed concern about the failure of Congress and the president to find a way to reduce large prospective budget deficits. He has said that the most important thing for a CBO director "is to have an open mind about different economic theorists and budget proposals."

Penner, who was born in Canada, holds an undergraduate degree from the University of Toronto and a doctorate in economics from the Johns Hopkins University.