Stephane Veilleux and Martin St. Louis scored first-period goals and Niittymaki protected the lead, giving up only a second-period goal to Todd White.
Thrashers star Ilya Kovalchuk broke his stick in frustration at the end of the game. He has no goals in the three games against Niittymaki this season.
The Lightning improved to 4-1 against the Thrashers this season with their fourth straight win in the series, including three victories with Niittymaki in the net.
Niittymaki, in his first season with the Lightning after five with Philadelphia, improved to 11-0 at Philips Arena.
Kovalchuk, the Thrashers' career leader in goals and assists, can become an unrestricted free agent on July 1 and is the subject of trade rumors. Atlanta general manager Don Waddell attended the Los Angeles Kings game at New Jersey on Sunday and was in Philadelphia last week scouting the Flyers and Islanders for potential trades.
Tampa Bay snapped a two-game losing streak and improved to 9-15-5 in road games. The Lightning began the night with only 21 points in road games, the fourth fewest in the NHL.
The Lightning led 2-0 despite recording only three shots.
Veilleux's shot from the left circle gave Tampa Bay its first goal midway through the opening period. St. Louis, set up by a pass from Steven Stamkos, scored the second goal past lunging goalie Ondrej Pavelec. Stamkos faked a shot before earning the assist.
Atlanta defenseman Mark Popovic, making his return after missing 27 games because of a broken foot, earned an assist on White's goal 2:46 into the second period to cut the lead to 2-1.
Pavelec stopped 22 shots for Atlanta.
NOTES: Niittymaki was also in goal for the Lightning's 2-1 home win over the Thrashers on Jan. 23 and a 4-3 win at Atlanta on Nov. 22. ... Thrashers F Slava Kozlov was a healthy scratch for the fifth straight game. ... Thrashers D Pavel Kubina played in his 800th game.