The Houston Texans, playing with a third-string rookie quarterback, held on for a 20-13 win at divisional rivals the Jacksonville Jaguars and the Chicago Bears' five-game winning streak ended against at Oakland.
Elsewhere, the New York Jets, Cincinnati Bengals and Atlanta Falcons all had scares before securing wins while the Indianapolis Colts, still without quarterback Peyton Manning, lost their 11th straight to remain winless on the season.
Brady was at his best, throwing for 361 yards while his opposite number Vince Young, standing in for injured Michael Vick, threw for a career-best 400 yards in vain.
The Eagles (4-7) started brightly with a LeSean McCoy two-yard touchdown run and a field goal before BenJarvus Green-Ellis ran in two touchdowns to give the AFC East-leading Patriots (8-3) a lead they would not relinquish.
Brady then picked out a wide open Wes Welker with a 41-yard touchdown pass and the pair combined again for a score in the third quarter to put the game out of reach, prompting chants from many Eagles fans to have coach Andy Reid fired.
Tim Tebow, whose credentials as an NFL quarterback remain questioned in many quarters, improved to 5-1 as a starter after leading Denver (6-5) to a 16-13 win in San Diego (4-7).
Matt Prater won the game with a 37-yard field goal late in overtime. Tebow went 9 of 18 for 143 yards and one touchdown and rushed for another 67 yards on 22 carries.
The AFC South-leading Texans, who lost quarterback Matt Schaub for the season due to injury two weeks ago, moved to 8-3 but suffered another setback as the Pro Bowler's replacement, Matt Leinart, left Sunday's game with a shoulder injury.
That meant rookie T.J. Yates had to step in, and with only recently signed backup Kellen Clemens as an alternative, the Texans may well be looking at quarterbacks again this week.
Leinart, making his first start since 2009, completed 10 of 13 passes for 57 yards and a touchdown before his injury and Yates kept things simple, relying on the Texans' quality running game, as he passed for 70 yards.
Arian Foster's one-yard run brought Houston level in the first quarter after Ashton Youboty scored on a fumble return for the Jaguars (3-8) less then two minutes into the game.
A 20-yard pass from Leinart to Joel Dreessen, followed by two field goals from Neil Rackers, put the Texans up 20-10 and Jacksonville, who struggled offensively all day, could only manage a field goal in the fourth quarter.
Buffalo Bills (5-6) wide receiver Stevie Johnson mocked Plaxico Burress's 2008 gun incident when he mimicked being shot in the leg after scoring a touchdown in a 28-24 loss to the New York Jets (6-5) in an AFC East showdown. [ID:nN1E7AQ0BA]
Matt Ryan had three touchdown passes for the Falcons, who led 17-0 over the Minnesota Vikings (2-9) at half-time but let their opponents back into the game with two touchdowns.
But Ryan's three-yard pass to Michael Palmer secured the 24-14 win for Atlanta, who improved to 7-4 in the NFC South.
The Carolina Panthers (3-8) snapped their 12-game winless run on the road thanks to a 27-19 win in Indianapolis (0-11).
Panthers rookie quarterback Cam Newton threw for 208 yards and ran in a touchdown while DeAngelo Williams rushed for two scores.
