Wigginton's two-run double in the third inning opened the game's scoring and his run-scoring single in the seventh off Mets reliever Bobby Parnell (1-1) broke a 4-4 tie, putting the Phillies ahead to stay.
The first baseman capped his big day with a three-run shot in the ninth as Philadelphia claimed the opener of a three-game set Citi Field.
John Mayberry added a two-run homer in the victory.
Cole Hamels (8-1) earned the victory despite yielding a pair of homers. The left-hander allowed four runs on seven hits, walking one and striking out six.
Vinny Rottino and Scott Hairston each delivered two-run homers for the Mets.