Lagares provided a run-scoring single in the first inning, when the Mets sent eight batters to the plate and built a 3-1 lead.
Gonzalez Germen (1-1) earned the decision with 1 2/3 scoreless innings in relief of Mets' starter Zack Wheeler.
Closer Bobby Parnell surrendered a two-run homer to Chase Utley and a two-out double to Domonic Brown in the ninth, but induced Darin Ruf to line out, ending the game with his 18th save as the Mets evened their three-game series.
Cole Hamels (4-12) was hung with the loss after allowing four runs on seven hits over five innings.
Utley finished with three RBI for the Phillies.
NBC reportedly holds celebs hostage to Jimmy Fallon's show
Ray Liotta sues skin care company over use of likeness