The Mets catcher initially stayed in the game after being evaluated by trainers and scored on a single from Harrison Bader, but was replaced by Omar Narvaez in the bottom half of the inning.
Chapman (0-1) was ejected by plate umpire Edwin Moscoso after Harrison Bader doubled in the eighth inning of the Pirates' 6-3 loss to the Mets.
The Mets rallied again to beat the Pittsburgh Pirates 6-3 in the series opener on Monday night at Citi Field.