Holmes caught four passes for 97 yards. Brunell, the backup to Mark Sanchez on the New York depth chart, played most of the game and completed 11-of-17 passes for 118 yards and two touchdowns.
The game featured two fumble returns for touchdowns, both by rookie Philadelphia defensive back Kurt Coleman. He had a 64-yard return in the first period and an 8-yarder in the second that gave the Eagles a 17-7 halftime lead.
The Jets scored the only points of the second half on a 14-yard run by Danny Woodhead and the Brunell-to-Holmes pass that came 43 seconds into the final period.
Both teams finished the pre-season with 2-2 records. The Jets will host Baltimore in a Monday night game to open the regular season. Philadelphia starts with a home game against Green Bay.