Cespedes pulled up lame after rounding first base on a one-hop double in the bottom of the fourth inning. He bent over in pain after reaching second as manager Terry Collins and head athletic trainer Ray Ramirez rushed out to see what was wrong.
Cespedes draped one arm over the shoulder of Ramirez and the other over the shoulder of first base coach Tom Goodwin as he limped slowly back to the Mets dugout.
The 31-year-old Cespedes, who has six home runs and 10 RBIs this season, had just returned to the lineup Wednesday after a nagging hamstring injury had sidelined him for three games.
Michael Conforto replaced Cespedes in Thursday’s game.
Syndergaard, who is 1-1 with a 1.73 ERA and 30 strikeouts in 26 innings this season, originally was going to pitch Wednesday but had been moved to Thursday.
He pitched through a bone spur in his right elbow through a large part of last season. Syndergaard said his biceps became irritated a few days ago and he took anti-inflammatory medication.
The Associated Press contributed to this report.