Lindor winced after grounding out to second base. He took a few steps out of the batter's box but then peeled off toward the Mets' dugout on the first-base side.
Accompanied by an athletic trainer, Lindor then headed down the tunnel toward the clubhouse.
Lindor was replaced by Luis Guillorme in the bottom of the fifth after going 1-for-3.
In his first season with the Mets after being acquired from the Cleveland Indians in a January trade, Lindor is hitting .228 with 11 home runs and eight stolen bases in 88 games. He agreed to a $341 million, 10-year contract just before Opening Day.
Lindor was a four-time All-Star with Cleveland while winning two Gold Gloves and two Silver Slugger awards.
Beset by a long list of injuries all season, the National League East-leading Mets just got third baseman J.D. Davis back from the 60-day injured list on Friday. Davis wasn't in the starting lineup, but his return gave New York all its projected regulars available for the first time in months.