The Justice Department filed suit yesterday against former representative John W. Jenrette, (D-S.C.), who was convicted two years ago of bribery and conspiracy charges in the FBI's undercover Abscam investigation.

What the Justice Department wants from Jenrette and a codefendant is nearly $50,000 in bribe money the two men allegedly accepted from undercover FBI agents. Of the $50,000 allegedly received by Jenrette and former Richmond businessman John Stowe, only $1,300 has been recovered, according to the suit. That money, in hundred-dollar bills, was part of the more than $25,000 Jenrette's former wife, Rita, said she she discovered in her husband's closet in a shoe box.

The suit yesterday is one of several filed against Abscam defendants by the government. The department so far has recovered no money. The suits have been stayed pending appeals of the convictions.

A spokesman for the U.S. Attorney's office said the goverment normally waits until the criminal trial ends before filing a civil suit. Jenrette has been free since his conviction pending a ruling on his request that the jury's verdict be set aside. Judge John Garrett Penn has had the request for two years, and given the time that has elapsed since the verdict, the government decided to go ahead with the suit. CAPTION: Picture, JOHN JENRETTE . . . $25,000 in the closet