Cespedes landed hard on his right knee and dislodged a huge divot in left field while trying to make a sliding catch in the sixth inning.
Collins and the team trainer came out to check on Cespedes on the field and decided to remove him from the game.
"I doubt he's going to be in there [Sunday], just as a precaution," manager Terry Collins said after the game.
Speaking through a translator, Cespedes said he has "a little" discomfort but that the doctor told him "there's nothing serious going on."
"I think I could have definitely kept on playing," he said. "It's just because of the score of the game we just decided to play it safe."
Cespedes returned from the disabled list on June 10 after missing six weeks with a strained left hamstring.
He is hitting .281 with nine home runs and 20 RBIs.
The Associated Press contributed to this report.
Cespedes leaves game after trying to make sliding catch
Yoenis Cespedes gets stuck in the grass, falling awkwardly, and would leave the game in the sixth inning.