"My hammy's been bugging me lately," Church said. "It's actually caused my torso on my right side to get out of whack. I just finally had enough."
Church, 30, was batting .272 with one home run and eight RBIs, splitting playing time with Gary Sheffield in right field. After flying out to lead off the top of the fourth inning, he jogged out to his position to warm up in the bottom of the inning, then returned to the dugout at Manuel's request.
Angel Pagan replaced him in right field.
"It was limiting me [from] going out there and giving everything I've got," Church said.
The Mets are already playing without starting shortstop Jose Reyes, who is battling tendinitis in his right calf; first baseman Carlos Delgado, who is recovering from hip surgery; and catcher Brian Schneider, who is on the disabled list with a strained back.
Anthony DiComo is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.