Wigginton hit a two-run double in the third, RBI single in the seventh then sealed the win with a three-run homer in the ninth for the Phillies, who have won five of their last six games. John Mayberry hit a two-run homer in the sixth to account for the rest of Philadelphia's offense.
Cole Hamels (8-1) won his fifth straight start and remained unbeaten since losing his first game of the season as he gave up four runs on seven hits with a walk and six strikeouts over eight innings. He went 5-0 over six starts in May and is the first eight-game winner in the majors.
Scott Hairston and Vinny Rottino each hit two-run homers for the Mets, who had a three-game winning streak snapped.
Jon Niese started on the mound for New York but didn't factor into the decision as he gave up four runs on two hits with five walks and seven strikeouts over five innings. Bobby Parnell (1-1) was tagged with the loss for giving up a run in the seventh inning.
Philly went on top by a run in the seventh. Jimmy Rollins started the finning with a single and moved to second on Placido Polanco's groundout back to the mound. After a Hunter Pence walk, Shane Victorino flied out, but Wigginton followed with a single to center for a 5-4 lead.
Hamels then set the Mets down in order in the seventh before getting out of a jam in the eighth.
Andres Torres greeted Hamels with a pinch-hit double to start the inning and moved to third on a Kirk Nieuwenhuis groundout. Daniel Murphy then grounded out to second as Torres was held at third, and David Wright grounded out to third to end the inning.
Wigginton blasted his fourth homer of the year in the ninth and Papelbon set the Mets down in order in the ninth to close the game.
The Phils plated a couple of runs in the third. With two outs, Pence kept the inning alive with a walk and Victorino followed suit with a free pass. Wigginton then punched an opposite field double to the gap in right-center to plate both runners for a 2-0 lead.
Hamels retired the first seven batters he faced until Rob Johnson hit a one- out single in the third. Following a sac bunt from Niese, Justin Turner punched a single to right.
Pence fielded the ball and came up firing and Johnson was held at third. Turner, though, was caught in a run down and eventually tagged out by Rollins. He planted his right foot awkwardly on the bag and had to leave the game after being helped off the field.
New York tied the game in the fifth as Lucas Duda led off with a walk and Rottino followed with a line-drive shot over the wall in left for his second home run of the season.
The Phils took the lead back in the sixth when Wigginton walked to start the frame and Mayberry followed with a big blast over the wall in left, but the Mets got the runs back in the bottom of the inning on a two-out, two-run homer from Hairston.
Mets shortstop Justin Turner left the game in the third inning with a right ankle sprain. David Wright shifted over to shortstop after Turner left the game. X-rays of the ankle came back negative.
-- Sports Network contributed to this report.