Lehtonen made a lunging glove save along the goal-line on Stamkos with 8:09 to play in the third. The play was reviewed by replay and the ruling on the ice was upheld.
"I felt like the puck was in the pocket of the glove right near my wrist," Lehtonen said. "He made a nice move. I thought he was going the other way. Then it was just desperation. It was tough. It could have gone either way."
Stamkos, taken first overall in last year's draft, felt he had his seventh goal taken away, but the rookie understands why the call wasn't reversed.
"When you look at the replay, you have to be able to see the whole puck," Stamkos said. "You can't see the puck although you know it's in his glove and you know it's over the line. I saw the puck in his glove go over the line."
"We kind of limited their options," Stuart said. "We tried to keep the shots outside and let Kari see them. I thought it was a good effort."
Gary Roberts scored for the Lightning, who have lost five of six. Rookie goalie Mike McKenna stopped 21 shots.
"Our goalie gave us a chance to win," Tampa Bay center Jeff Halpern said. "We, as a team, dropped the ball."
Tampa Bay interim coach Rick Tocchet said some of his players were "disinterested" early on. The Lightning are 12th in the Eastern Conference.
"Just not interested," Tocchet said. "Maybe it's the coaching staff's fault. I don't know. We're pretty disappointed in some guys."
Kozlov, playing in his 1,100 NHL game, gave Atlanta a 2-1 lead at 2:02 of the second. The goal was the 340th of the his career.
Kovalchuk scored an empty-net goal with 9.1 seconds remaining.
Roberts put the Lightning up 1-0 at 1:24 of the first on his 438th career goal. Atlanta tied it at 1 when Stuart scored a short-handed goal with 10:08 left in the period.
Kovalchuk has one goal and one assist in four games this season against the Lightning. ... Tampa Bay recalled D Josef Melichar from Norfolk of the AHL. LW Wade Brookbank was assigned to Norfolk. ... Thrashers D Niclas Havelid assisted on Kozlov's goal for his first point 16 games. ... Lightning D Marek Malik (ankle) returned after missing the previous nine games. D Paul Ranger didn't play due to an upper-body injury.