A fan who attended a game between the Braves and the San Francisco Giants alleged McDowell taunted three other men with homophobic remarks and actions at AT&T Park last month and then threatened him when he objected.
Baseball Commissioner Bud Selig said in a statement McDowell has been suspended for two weeks without pay retroactive to April 29 and has been assessed an undisclosed fine.
"Conduct by people associated with MLB that shows insensitivity to others simply cannot and will not be tolerated," Selig said. "I understand that Mr. McDowell is very contrite about his conduct, and hopefully this incident will be used to increase public awareness of the importance of sensitivity to others."
Selig said McDowell, who will participate in a sensitivity training program, will make a direct apology to those involved.
The fan, Justin Quinn of Fresno, Calif., said he and his twin 9-year-old daughters heard McDowell taunt the three men, allegedly saying, "Are you guys a homo couple or a threesome?" then grabbing a baseball bat and using his hand to crudely simulate sex.