Also signing a new deal was assistant general manager Tony Siegle.
Bowden, 44, and Manager Frank Robinson put together a team that compiled a record of 81-81 in the Nationals first season in the nation's capital from Montreal. Their 14-game improvement matched the Brewers for the third largest in baseball.
Bowden's status was always in limbo because the Washington franchise is run by Major League Baseball and a new owner has been sought for over a year. The team said on its Web site that a new deal has been in the works for several weeks. Bowden was working on a six-month contract, which was set to expire on April 30.