Baker held his usual pregame availability with the media about two hours before the 7:10 p.m. game. The announcement of the positive test came after the game started.
Baker, 73, is in his third season as Houston's manager. Bench coach Joe Espada filled in for Baker against Cleveland.
The Astros (70-38) lead the AL West by 12½ games over Seattle.
The Associated Press contributed to this report.