Kendrick (8-5) scattered six hits and a walk while notching four strikeouts to pace the Phillies to the rubber match victory. Brad Lidge earned his 16th save.
Philadelphia has now won 18 of its last 23 games to tie San Francisco atop the wild card standings. The Phillies and Giants, who lost Sunday, start a three-game set with San Francisco Tuesday at Citizens Bank Park.
Mike Pelfrey (11-7) gave up three runs on seven hits in seven innings.
The Mets' only run came on a Jose Reyes home run.
New York has lost 10 of its last 13 series (2-10-1).