Niittymaki stopped 23 shots to stay perfect in eight decisions against the Thrashers and Steve Downie scored with 4:29 left in the third period to give Philadelphia a 3-2 victory on Tuesday night.
The Flyers' No. 1 goalie, Martin Biron, has a five-game winning streak, but Niittymaki's streak of success against the Thrashers earned him the start.
"Marty has played so well at home, but we just targeted this game for Niitty," Philadelphia coach John Stevens said. "He seems to play his best games against Atlanta. He really elevated his game. ... I thought he was terrific."
Niittymaki has allowed only 13 goals while going 8-0 against the Thrashers.
"It's just something about this building," Niittymaki said of Philips Arena. "I like to play here. It's one of those things where you feel comfortable playing some teams and you get good bounces, too."
One of those fortunate bounces for Niittymaki and the Flyers came only 30 seconds after Downie's go-ahead goal. A video review confirmed a shot by Atlanta's Marian Hossa hit the post to Niittymaki's left and did not cross into the net.
Niittymaki remained undefeated as a pro against Atlanta's Kari Lehtonen, another native of Finland.
"I don't really think about playing against Lehtonen," Niittymaki said. "It's always nice to play another Finnish goalie. Maybe it gives you a little extra boost. You never want to lose to your countryman but still it's just one game and you try to win."
Philadelphia moved two points ahead of New Jersey and Pittsburgh for the Atlantic Division lead.
The Flyers have won nine straight against the Thrashers. They are 13-2-1 all-time at Atlanta and overall have won 24 of 30 games in the series, including three games this season.
The Flyers are 17-10 away from Philadelphia this season.
"We're playing good on the road," Downie said. "We want to keep it going."
A 2-2 tie after the second period lasted through the first 15 minutes of the third period. Scott Hartnell passed to Downie from behind the net, and Downie scored on a slap shot from about 25 feet for the go-ahead goal.
Downie's goal was the only one of the night for the Flyers that did not come on a power play.
The Flyers boast the league's second-best power play (24.7 percent), while the Thrashers are No. 27 with a 79.4 percent rate on the penalty kill. As the Thrashers' minors began to stack up, those stats become more important.
The Flyers took advantage of their first opportunity with a man advantage. Atlanta's Jim Slater drew a hooking penalty 1:04 into the game, and 35 seconds later Knuble deflected Richards' shot past Lehtonen for a 1-0 lead.
Knuble was coming off his first career hat trick in a 3-0 win over Anaheim on Saturday.
The Thrashers pulled even at 1-1 on Kovalchuk's goal 8:56 into the second. Kovalchuk showed no sign of a sore knee as he used his speed to skate past Randy Jones and Derian Hatcher before scoring his 39th goal.
The Flyers answered only 29 seconds later, again taking advantage of an Atlanta penalty.
Atlanta's Niclas Havelid was called for interference 9:21 into the second, and four seconds later Richards scored off the face-off.
The Flyers were 2-for-7 on the power play. The Thrashers were 0-for-3.
"We did take too many penalties, there's no doubt about it," Thrashers coach Don Waddell said. "We can't continue to take penalties like that, especially against good teams."
Boulton scored with only 1:22 left in the second. His shot through a crowd tied the game at 2-2.
The Thrashers had a three-game winning streak end. ... The Thrashers' last win in the series was on Nov. 18, 2005, when they won 6-5 in overtime in Philadelphia. ... The Flyers have won three games against Atlanta this year by a combined score of 11-3.