Charles F. Ruff, the last of the Watergate special prosecutors, will rejoin the Justice Department soon as the top assistant to Deputy Attorney General Benjamin R. Civiletti.

Ruff, 39, has been deputy inspector general for the Department of Health, Education and Welfare the past 15 months, since overseeing the end of the Watergate task force.

"I'm looking forward to going back to being a lawyer again," Ruff said in a telephone interview yesterday. At HEW he has concentrated on devising methods to attack fraud in programs such as Medicald and Medicare.

Ruff will assume his new post as chief associate deputy attorney general Sept. 5, a Justice Department announcement said yesterday.

A graduate of Columbia Law School, Ruff has been a law professor and an attorney in the department's criminal division. In 1973 he joined the Watergate special prosecution force.

After a short assignment as acting chief inspector at the then-troubled Drug Enforcement Administration in 1975, he was appointed the fourth and final Watergate special prosecutor.

His role became controversial in 1976 because of an investigation of President Ford's campaign finances just before the presidential election. Sen. Bob Dole (R-Kan.) held up Ruff's appointment to the HEW position last summer because he said he felt Ruff stalled on clearing Ford until just before the election loss to Jimmy Carter.

After in Watergate experience, Ruff said he was adamantly opposed to the idea of a permanent special prosecutor because of its potential for abuse and the morale problems it caused for the career Justice prosecutors.

Ruff affectionately has been called "Ironside" at time by Justice colleagues because he, like the Raymond Burr television character, is confined to a wheelchair.

Paul R. Michel, another member of the Watergate special prosecution force, also was recently named as a top aide to Civiletti. Most recently Michel headed the Justice Department's investigation of South Korean influence-buying on Capitol Hill.