The Eagles returned two kicks for touchdowns in the last 1:35 of the first half, Donovan McNabb led three long drives, and backup Kevin Kolb directed a 90-yard march to David Akers' second field goal on their opening series of the third quarter.
By that time, it was 27-3 and Matt Cassel was done for the night after failing for the third straight game to show that he deserved to remain as backup to Brady, last season's NFL MVP.
Cassel completed 8 of 14 passes for 60 yards and hasn't led a touchdown drive on any of his 15 series, although starting linemen Matt Light and Stephen Neal have been sidelined all three games. Cassel hobbled off after being sacked on his last play with about 10 minutes left in the third quarter.
Second-year pro Matt Gutierrez took over and did much better with fourth-quarter touchdown passes of 1 yard to Chad Jackson and 6 yards to C.J. Jones against backups.
Brady's injury does not appear serious and he could be ready for the season opener against Kansas City. The Patriots (0-3) were unbeaten in the regular season last year then won two playoff games to go to 18-0 before losing the Super Bowl to the New York Giants.
While Cassel, entering his fourth season, struggled, five-time Pro Bowler McNabb rebounded from an unproductive game to go 13-for-17 for 180 yards and a 7-yard touchdown pass to Jason Avant.
The Eagles (2-1) beat Carolina 24-13 in their previous game, although McNabb and the first-team offense were scoreless in six possessions.
McNabb missed two games last season because of ankle and thumb injuries but led the Eagles to wins in their last three games that left them at 8-8 and out of the playoffs. He also missed some offseason practices with a shoulder injury.
Leading 10-0 Friday, he nearly threw a 7-yard scoring pass to Hank Baskett. But Patriots coach Bill Belichick challenged, and replay officials ruled Baskett lost the ball before crossing the goal line and it went out of bounds, giving New England a touchback.
The Patriots managed a 35-yard field goal by Stephen Gostkowski on the next series - with the big play a 47-yard gain on a defensive pass interference call.
Then it was the special teams' turn to collapse.
Philadelphia's Quintin Demps returned the kickoff 101 yards for a touchdown. And when Cassel couldn't get a first down on the next possession, DeSean Jackson ran back Chris Hanson's punt 76 yards for another touchdown on the final play of the half, making it 24-3.
Belichick threw his headset to the ground and bellowed at Hanson on the sideline.
The Patriots could have another problem. Wes Welker, who tied for the NFL lead with 112 receptions last season, left with a rib injury in the second quarter and didn't return.
An early sign of the Patriots' futility came on their first offensive play when Randy Moss was thrown for a 5-yard loss on an end around. The tackler? Former Patriots Pro Bowl cornerback Asante Samuel, who signed a $58 million, six-year contract with the Eagles in the offseason.
Now the Patriots have just one more game to get things straightened out before the regular season - an exhibition against the Super Bowl champion Giants next Friday.