Brady, making his first appearance since a knee injury ended his 2008 season in the first game, threw two touchdown passes to tight end Benjamin Watson in a span of 66 seconds to spark the dramatic late win in their 2009 opener.
Brady hit Watson with an 18-yard TD pass with 2:06 left and, after Buffalo's Leodis McKelvin fumbled the ensuing kickoff away at the Bills' 31, threw three straight completions, highlighted by a 16-yarder to Watson to seal victory.
"I'm glad it's over, glad we're moving on—got a win and we'll learn from it," Brady told reporters after his 29th career comeback victory.
The Patriots failed on two-point conversions after both scores but Buffalo could not recover and suffered a 12th straight defeat against New England.
Brady finished 39-for-53, 378 yards in addition to the touchdowns and was 12-for-14 for 112 yards on the last two possessions.
Rival quarterback Trent Edwards threw for two touchdowns and played a strong game to almost lead his team to victory, but the Patriots and Brady refused to go away.
Brady looked rusty at times early but warmed up as the game wore on. He threw eight straight completions on one third-quarter drive that came up empty and then completed five in a row on the next drive before the Patriots settled for a field goal.
"I felt good," Brady said. "I felt good all night. We were just off."
Receiver Randy Moss tied his career high 12 catches, a number matched by fellow receiver Wes Welker.
Buffalo defensive end Aaron Schobel returned a one-handed interception of a screen pass 26 yards for a first-half touchdown, helping the Bills to a 14-10 halftime lead.
New England's win came at a cost, however, as they lost second-year linebacker Jerod Mayo early with an apparent knee injury.
Wide receiver Terrell Owens caught two passes for 46 yards on his Bills debut.
The game kicked off the 50th season of both teams.
The New England Patriots called themselves the Boston Patriots on Monday and both teams wore throwback uniforms of that day.
