Both are suspended for one game following an run-in during the 8th inning of the Phillies/Astros game on Tuesday.
Manuel's suspension is to be served Friday night when the Phillies are to host the Boston Red Sox.
Umpire Bob Davidson will also serve his suspension Friday night. His crew will work the Minnesota Twins-Milwaukee Brewers game at Miller Park.
Davidson was suspended "for his repeated violations of the Office of the Commissioner's standards for situation handling," a statement from MLB read.
Manuel was ejected in the eighth inning of a 4-3, 10-inning win over Houston. He thought a ball had been foul tipped and got into an argument with Davidson that escalated into profanities.