Coming off a 3-2 loss in a shootout Friday at Tampa Bay, Atlanta won for the second time in three games.
Lehtonen, who allowed Dan Boyle's game-tying goal with 11 seconds left in overtime the night before, made 12 saves in the third period.
The Thrashers' goaltender improved to 4-0 against Florida this season after Panthers centre Stephen Weiss missed the net on a wide-open shot from the right side.
Weiss' nine-foot attempt came after Joe Nieuwendyk beat Bobby Holik on a faceoff that began a three-man advantage for Florida.
The Panthers, who have lost three straight and six of eight, failed to take a shot on goal in the final nine seconds even though Atlanta's Brad Larsen and Kovalchuk were sitting in the penalty box.
Panthers coach Jacques Martin pulled goalie Alex Auld, who stopped 27 shots, with 52 seconds left.
Despite entering with the NHL's second-best power-play unit, the Panthers dropped to 1-for-23 against Atlanta after failing on seven chances.
Kovalchuk was inside the blue-line when he skated past Bryan Allen for a breakaway. Taking Scott Mellanby's pass from the right boards, Kovalchuk fired a long wrister between the circles to Alex Auld's glove side 13:43 into the first period.
In four games against the Panthers this season, Kovalchuk has seven points, including five goals.
Notes: Florida dropped to 2-7-3 on the road. ... Early in the second period, the goal light went on, but the officials called for a replay that confirmed Lehtonen ended the play by smothering the puck before it went into the net. ... Atlanta improved to 13-3-2 when Kovalchuk has a point. ... Thrashers coach Bob Hartley won his 300th career game.