Jay Pandolfo added an empty-net goal with 15.6 seconds remaining, and Brodeur made 14 saves to earn his 45th win.
"It was a battle," Brodeur said. "The ice was terrible once again. We pulled it off. We didn't start the way we wanted, but we were able to get out of the first period 0-0. After that, I thought we took over the game."
The victory ended the Devils' five-game losing streak at home and moved New Jersey into a tie with the Pittsburgh Penguins atop the Atlantic Division. The Penguins and Devils each have 100 points with four games to play.
The Devils continued their mastery of the Flyers, improving to 6-1 against Philadelphia this season. New Jersey has won eight straight over Philadelphia at the Continental Airlines Arena.
Brodeur tied Vancouver's Roberto Luongo for the NHL lead with 45 wins, two shy of Bernie Parent's league record for a single season.
Simon Gagne scored for the Flyers, who have dropped five of their last six.
The Devils started slowly. The Flyers had the better of the play over the first 30 minutes before the Devils tightened up defensively and finally pressured goalie Martin Biron.
Rupp broke a scoreless tie with 1:20 left in the second as he tipped in Brad Lukowich's point shot.
"We started playing well and we finally started getting the puck behind their defense and getting in there," Rupp said. "That's our game plan against them, and everybody."
Zajac notched a power-play goal with 9.9 seconds remaining to give the Devils a 2-0 lead. Brian Rafalski fired a shot from the blue line that Biron blocked. Zach Parise swiped at the rebound, but couldn't control it before Zajac swooped in and scored.
"He didn't have much room to put it in," Biron said. "He had maybe eight inches to get a backhand into the net. Those were a couple of tough goals to fall behind."
Brodeur lost the bid for his 13th shutout of the season when Gagne scored his 38th goal with 5:57 remaining. Gagne drilled Mike Knuble's rebound over Brodeur's left shoulder.
It was one of only two shots the Devils allowed in the final period.
The Flyers dominated the action in the scoreless first period. Philadelphia had several excellent scoring chances, but none better than one by R.J. Umberger with 11 minutes remaining. Umberger had a lot of net to hit from the bottom of the right circle, but Brodeur nimbly slid across to make a pad save.
- C John Madden returned for the Devils after missing seven games with a groin injury.
- With Madden back, the Devils assigned RW David Clarkson to Lowell of the AHL. Clarkson scored three goals in seven games since his call up on March 15.
- The Devils regained a center -- Madden -- but lost one when Scott Gomez suffered a bruised thigh and did not return for the third period after taking only one shift in the second.
- The game kicked off a three-game homestand for the Devils. They host Boston Sunday and Ottawa on Tuesday.
- The Flyers were without D Denis Gauthier (wrist), RW Scottie Upshall (shoulder) and C Mike Richards (shoulder).