He finished 7 for 11 for 26 yards, and carried the ball seven times for 35 yards.
Vick, released from federal custody July 20 after serving 18 months of a 23-month sentence for his role in operating a dogfighting ring, will be eligible to play Sept. 27 against Kansas City, commissioner Roger Goodell said earlier Thursday.
Jets rookie Mark Sanchez looked sharp, completing all five of his passes, and capped his only series with a 21-yard touchdown pass to Jerricho Cotchery. Danny Woodhead, making a bid to make the team, ran for 158 yards and two touchdowns.
After David Akers kicked a 36-yard field goal to make it a four-point game, Erik Ainge threw a 73-yard touchdown pass to David Clowney to make it 38-27 with 4:51 remaining.
Booed each time he ran onto the field in the first half, Vick has scored his first NFL touchdown since the 2006 season, giving the Eagles a 14-7 lead early in the second quarter.
Playing in his second game with the Eagles, Vick lined up at quarterback, faked a handoff and ran up the middle from 2 yards out 25 seconds into the quarter. It was really the only highlight of the game after an important day for Vick, who met with Goodell a few hours before the game and was told he could play starting in Week 3.
Vick entered the game on the Eagles' third play from scrimmage to mostly boos from the Meadowlands crowd and took a direct snap and ran 2 yards for a first down. One play later, he lined up at quarterback.
There were no notable protests outside the stadium, but two fans made their displeasure known, one holding a placard that read "Watch Your Beagle," while the other one said, "Vick Is An Eagle."
Vick was in and out of the lineup in the opening half, and was intercepted on his first pass of the first half. His toss intended for Jeremy Maclin was slightly underthrown from 36 yards as Dwight Lowery picked it off.
He opened the second half as the quarterback, but his feet also got him in trouble, losing 22 yards when he tried to scramble on third down in the third quarter. He kept losing yardage before he was sacked by Jamaal Westerman at the 4-yard line. Vick also lost the ball on the play before recovering.
The Eagles were forced to punt, and it set up the Jets' go-ahead score as Woodhead ran for a 3-yard TD.
Vick started practicing with the Eagles on Aug. 15. He played six snaps in Philadelphia's home game against Jacksonville, lining up at quarterback and receiver. He completed all four of his pass attempts, but the Eagles' offense scored just three points in the possessions he played.
Donovan McNabb, Brian Westbrook and most of the Eagles' other starters didn't play in this one, while most of the Jets' starters on offense and defense played one series.
Eagles rookie LeSean McCoy gave Philadelphia an early 7-0 lead with a 1-yard run.
Woodhead, who missed last season with a knee injury, had a 55-yard touchdown scamper in the second quarter. He took the handoff up the middle, maneuvered through traffic, kicked outside and took off down the right sideline to make it 14-14.
Kevin Kolb, who started at quarterback, connected with Tony Curtis on a 12-yard touchdown pass to give Philadelphia a 24-14 lead with 1:03 left in the half.