Niittymaki made 37 saves, including three strong stops during overtime, and improved to 15-0 against Atlanta.
"I can't explain it," Niittymaki said.
Steven Stamkos netted Tampa Bay's only goal. The Lightning have won six of their last eight home games.
"It's nice to find a way to win when you didn't play your best," Tampa Bay coach Rick Tocchet said. "He [Niittymaki] was incredible. He got us the two points."
"Moose [Hedberg] played unbelievable, and we had a lot of point-blank chances on Niittymaki," Thrashers center Rich Peverley said.
Tampa Bay's Kurtis Foster had a fourth-round shootout goal disallowed after a video review. After his initial shot was stopped by Hedberg, the puck went off his leg and into the net. A shooter is not allowed to score a rebound goal during the shootout.
Atlanta left winger Slava Kozlov was a healthy scratch, which ended his franchise record of 251 consecutive games. He has not scored in 16 games.
Antropov put the Thrashers ahead at 5:23 of the first period.
Stamkos tied it at 1 during a power play just over two minutes later. The goal came after Atlanta defenseman Pavel Kubina -- who was given an interference penalty on the play -- and Lightning forward Martin St. Louis collided in the Thrashers' zone.
"We had control of the game pretty much the whole way," Atlanta coach John Anderson said. "The goal they scored was a 4-on-3. That was a phantom call. He ran into our guy and we got a penalty."
Anderson was also "not happy" coming away with only one point.
"We don't get the two and we give a team that's right behind us the chance to tie us," Anderson said.
Atlanta and Tampa Bay, the 12th- and 13th-place teams in the Eastern Conference, are three points behind the eighth-place New York Rangers.
Thrashers G Kari Lehtonen (back surgery) started a conditioning assignment with Chicago of the AHL. He stopped 32 of 37 shots in a game against Peoria. ... Stamkos has five goals and 10 points in 10 games against Atlanta. ... Tampa Bay rookie D Victor Hedman was back in the lineup after being a healthy scratch for Thursday's game with Toronto.