Harper drew a bases-loaded walk as a seventh-inning pinch-hitter to cap a three-run outburst to widen the Phillies' advantage to 10-6.
Phillies manager Gabe Kapler said Harper is considered day-to-day and could start Monday night at home against Atlanta.
The Phillies ended the day two games behind the Chicago Cubs for the second NL wild-card spot.
Harper hasn't started since being hit by a fastball from Mets lefty Steven Matz on Friday night. X-rays were negative.
Harper is hitting .254 with 30 homers, 101 RBIs and an .869 OPS, including 12 homers and a .965 OPS in 30 games since Aug. 1.
The Associated Press contributed to this report.