He has maintained his innocence in the matter, but said Sunday, "I've become a distraction."
Seated at a table with Nationals president Stan Kasten in front of reporters and team officials, Bowden read from a prepared statement, sometimes deviating from the script as he struggled to contain his emotions.
No replacement was immediately announced.
Bowden is the only GM the Nationals have had since the franchise moved from Montreal to Washington before the 2005 season, overseeing a team that went 81-81 in that debut season but has been below .500 ever since. They went 59-102 last season.
YANKEES: Alex Rodriguez met Sunday with Major League Baseball officials, who wanted to interview the slugger about his admission that he used performance-enhancing drugs from 2001-03 with Texas.
The commissioner's office released a statement saying Rodriguez was cooperative in a two-hour interview with officials from MLB's Department of Investigations and Labor Relations Department.
No further details were revealed, and the statement said the commissioner's office would have no additional comment at this time.
DODGERS: The team has pulled its $45 million, two-year offer to Manny Ramirez , and owner Frank McCourt said negotiations will have to start again from scratch.
The Dodgers announced last week that Ramirez had declined the team's latest offer, a $25 million one-year contract for the 2009 season with a $20 million player option for 2010. McCourt said no talks with Ramirez's representatives were scheduled for Sunday.
METS: Ace Johan Santana said he was OK after throwing a bullpen session Sunday morning, and the team decided against sending him to snowy New York for an MRI on his balky left elbow.
"He'll be seen by our doctors when they come down," general manager Omar Minaya said.
The 29-year-old Santana long-tossed with new closer Francisco Rodriguez before heading to the bullpen for a 15-minute session with catcher Omir Santos .
ORIOLES: Left-hander Rich Hill was scratched from Sunday's spring training start against Washington with elbow stiffness. Hill made only five starts last year.