The Eagles (1-2) scored three second-quarter touchdowns, including Darren Sproles' 89-yard punt return, to take a 24-0 lead before the Jets (2-1) came to life.
Fitzpatrick was 35-for-58 for 283 yards with two touchdowns. He didn't get any help from the Jets' running game, which was held to 47 yards.
The first Jets TD came late in the first half, when Fitzpatrick hit Brandon Marshall with a 16-yard TD pass.
Earlier, Marshall lost the ball at the Jets' 43 when he tried to lateral the ball to teammate Jeff Cumberland at the end of a 15-yard reception. But the lateral hit an Eagles defender and was recovered by Jordan Hicks, who returned it 11 yards.
Sproles got his second TD soon after, a 1-yard TD that gave Philadelphia the 24-0 lead.
A scoreless third quarter included Fitzpatrick's first interception, Eric Rowe's pickoff in the Eagles end zone.
Fitzpatrick threw a 7-yard TD pass to Jeremy Kerley with 9:37 left to cut it to 24-14 and soon after David Harris forced a Ryan Mathews fumble with 7:23 left at the Eagles 41. But three plays later, Brandon Bair tipped a Fitzpatrick pass that was intercepted by Walter Thurmond.
The Jets got the ball back and Nick Folk kicked a 53-yard field goal with 2:37 to go. But the Jets couldn't recover the onside kick. Even after two Eagle procedure penalties following their final timeout stopped the clock, a hands-to-the-face call on the Jets' Quinton Coples ended any chance of a Jets comeback.
Mathews, playing for the injured DeMarco Murray, ran 25 times for 108 yards for the Eagles. QB Sam Bradford was 14-for-28 for 110 yards and a touchdown, a 23-yard pass to Mathews that made it 17-0 with 4:48 left in the first half.
Marshall had 10 catches for 109 yards and became the first Jet since Laveranues Coles (2006) to have consecutive 100-yard receiving games.
The Jets travel to London to meet the Dolphins next Sunday at Wembley Stadium (9:30 a.m.).
[sny-editorial userid="BrianBassett"]I couldn't get on board the runaway enthusiasm floating around the Jets after their Monday night win over the Colts and this game was the reason why.
The Eagles are a talented team and their 0-2 record didn't properly reflect their abilities. If the Jets could stand on the throat of a wounded Eagles team, then you would have my attention.
The Jets could never get it going against a talented but struggling Eagles team. The weight of the world seemed to be on the shoulders of the Eagles and in a "back to the wall" situation; what was clear on Sunday was that Philadelphia wanted it more than the Jets and bested the Jets in all the right places.
Darren Sproles is just the sort of player who can routinely kill the Jets and that's just what he did. Philadelphia's offense found a little more life running behind Ryan Mathews than it had for DeMarco Murray.
Eagles receiver Jordan Matthews went off for six catches in the first half until the Jets keyed on him. The final score doesn't come close to reflecting how outmatched the Jets were by the Eagles.
After dominating the Colts on Monday night, the Jets looked flat for much of the first half and were unable to get onto the scoreboard until just prior to the half.Next week the Jets travel to London for their divisional matchup against the Dolphins.
At 2-1, the Jets have looked solid but still with flaws offensively and defensively. Let's hope the Jets can rest up and look sharp next week and regain the momentum from the win over the Colts. A 3-1 record will be on the line in London.