Niittymaki is one of only two active goalies with a perfect mark in at least 10 decisions against one team. Detroit's Chris Osgood is 17-0 against Tampa Bay.
Scott Hartnell, Darroll Powe and Randy Jones also scored, and Jeff Carter had two assists. Philadelphia, 13-1-2 in its last 15 home games, has beaten the Thrashers 13 straight times over parts of four seasons.
Eric Perrin, Ilya Kovalchuk and Chris Thorburn scored for Atlanta.
Knuble put in his own rebound at 12:12 of the third period after the Thrashers battled back from a 3-0 deficit. He added an empty-net goal with 40.5 seconds left.
Hartnell put the Flyers ahead at 9:54 of the first period with his 17th goal. He picked up a loose puck and scored on a backhander while sliding on his knees.
Powe made it 2-0 at 17:55 of the period by poking in another backhander after taking a cross-ice pass from Scottie Upshall. It was Powe's second goal of the season and first in 18 games.
Jones ended a 17-game goal drought. He backhanded a rebound that bounced off the glass to the right circle 1:44 into the second period to put the Flyers ahead 3-0.
Atlanta scored three goals in a 6:07 span in the third period to tie it.
Perrin scored at 4:42, picking up a loose puck and scoring on a slap shot from the right circle. Kovalchuk scored on a wrist shot at 9:48, and Thorburn tied it 1:01 later when he stole the puck from Randy Jones and skated in on a breakaway.
Thrashers goalie Kari Lehtonen can't stop a score by Philadelphia Flyers' Darroll Powe (AP Photo/H. Rumph Jr)
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