After getting hit with a 93-mph fastball from Pirates starter Juan Nicasio, Flores was checked out by trainers before staying in the ballgame.
The Mets third baseman fielded a ground ball cleanly in the top of third and got Eric Kratz with a throw to first, but between innings, Flores tried unsuccessfully to hit in the batting cages. Kelly Johnson then pinch-hit for Flores in the bottom half of the frame.
"I tried to swing," Flores said. "But I felt that my hand was so weak that I couldn't go."
Flores later said that he hopes to play Friday, and he does not believe the injury is one that should keep him out for "more than two days."
Flores has hit .375 (15-for-40) since taking over for David Wright, who underwent neck surgery Thursday.
Troy Provost-Heron is a reporter for MLB.com based in New York. This story was not subject to the approval of Major League Baseball or its clubs.