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.
"I got a little sloppy in the first 10 minutes of the third period and they got back in the game," Niittymaki said. "But Knuble had some big shots for us."
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.
Knuble scored the winner on a "busted play" coming through the neutral zone.
"Mike [Richards] slipped the puck through the crowd to me," Knuble explained. "I just got one quick shot. It wasn't a great shot, but it bounced right back to my stick and I knew I had an open net."
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.
"We all were a little bit disgusted because we're better than that and we had the game in our hands," Knuble said about the Flyers' third-period letdown. "It was just a little bit of sloppy play by us. It started in the second when it got a little bit loose. We have to close these games out."
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 coach John Anderson said that he was disappointed, especially after the Thrashers scored three goals in a 6:07 span in the third period to tie it.
"It's unfortunate," Anderson said. "We hit a few posts, missed on a round of breakaways. We were creating chances. It's disappointing. I thought we played well enough at least to get a point."
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 Jones and skated in on a breakaway.
"We made a commitment there in the third to get the puck to the net," Thorburn explained. "You see what can happen when we can do that."
Upshall said that Flyers coach John Stevens told the team to settle down and "refocus" during a 30-second timeout following Atlanta's comeback.
"Johnny says, 'Boys, keep it simple," Upshall said. '"We've been playing great all game. Just get back to the simple things. We'll win this game.' It obviously worked."
Flyers C Daniel Briere will undergo exploratory surgery Thursday for lingering discomfort in his groin and stomach area. He will miss at least another two weeks. ... Philadelphia is 25-4-6 overall against Atlanta. ... Carter extended his points streak to five games (three goals, four assists).