Trailing 24-3 at the half, the Eagles (10-4) staged a furious comeback, scoring 24 points in the fourth quarter alone to take over first place in the NFC East.
On the game's final play, Matt Dodge kicked a line-drive punt that Jackson fumbled initially. But he then picked up, burst up the middle and weaved his way down the right sideline for a 65-yard score as time expired.
Philadelphia racked up four touchdowns in the final 7:28 to pull off the miracle finish, with Michael Vick (21-of-35, 242 yards) tossing TD passes to Brent Celek and Jeremy Maclin and rushing four yards for a score in the outburst.
Vick carried the ball 10 times for 130 yards in the victory.
The Giants, meanwhile, fell to 9-5 and saw their three-game winning streak snapped.
Eli Manning gained 289 yards on 23-of-39 passing, with four TDs and one interception in the stunning loss.