Regular shortstop Jose Reyes is likely to return for the series opener against the Dodgers.
Cora, 33, injured his thumb sliding into second base on a first-inning double. He remained in the game for another two innings, but did not join his teammates on the field for the bottom of the third.
"There were certain plays I couldn't have made," Cora said. "I'm not going to put my team in a bad situation. If they hit the ball in the hole, I could have cost them the game."
Cora had been starting at shortstop in place of Reyes, who has missed the past four games with tendinitis in his right calf. The Mets are not completely sure how much more time Reyes will need to recover, though manager Jerry Manuel offered a shot of confidence after the game.
"I think Jose will be ready," Manuel said.
Replacing Cora at shortstop was Fernando Tatis, a third baseman-turned-outfielder who had played just three previous games at shortstop in a 10-year career. Tatis hadn't played a game there since Sept. 13, 1998, with the Cardinals and has played just eight big league innings at the position.
Tatis has now played at every spot on the diamond this season other than pitcher, catcher and center field.
"My team needed me over there," Tatis said. "I feel pretty comfortable. That's my role."
Cora was batting .333 with nine runs and three steals prior to the injury and had made just one defensive error in 108 innings, split between three positions.
Anthony DiComo is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.