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.