Eric Young Jr. singled, doubled and drove in a run for the Mets, who have won four of seven.
Darin Ruf doubled and drove in a pair of runs for Philadelphia, which has lost four of seven.
LaTroy Hawkins pitched a scoreless ninth for his 11th save in 14 opportunities. Hawkins got some help when a retreating Juan Lagares made a leaping, one-handed catch in front of the wall in center to rob Ruf of extra bases leading off the inning.
The Mets jumped on Cole Hamels for three runs in the first. After Young led off with a bloop double that bounded off the glove of diving right fielder John Mayberry Jr. and Murphy singled, Wright homered in his first at-bat since being placed on the disabled list Aug. 3 with a strained right hamstring.
The homer moved Wright past Mike Piazza into second on the club's career list with 221 homers. Darryl Strawberry is No. 1 with 252.
New York added lone runs in the third and fourth on RBI singles by Andrew Brown and Young, respectively, before the Phillies scored four times in the bottom of the fourth to pull within 5-4. Ruf did the bulk of the damage with a two-run double. Hamels also drove in a run with a groundout to first.
But the Mets got an insurance run in the seventh on Josh Satin's RBI groundout.
Matsuzaka (2-3) pitched six innings, allowing four runs on four hits with six strikeouts and three walks.
Hamels (8-14) lost for the first time since July 26. The left-hander entered Friday 4-0 with a 2.18 ERA in the nine starts since his last defeat. But he left after seven subpar innings, giving up six runs on 10 hits with eight strikeouts and no walks.