McAmmond took a pass from Jason Spezza and beat Atlanta goaltender Kari Lehtonen to give the Senators their first win in three games between the teams this season.
Mike Comrie had scored earlier in the third before a crowd of 19,881 at sold-out Scotiabank Place.
Chris Kelly, who scored short-handed and had an assist, Peter Schaefer and Mike Fisher, into an empty net, had the other goals for the Senators (34-22-3).
Spezza and Daniel Alfredsson finished with two assists and Martin Gerber made 28 saves for Ottawa, which gave coach Bryan Murray career win No. 599. Only four coaches in NHL history have reached the 600-victory plateau.
Slava Kozlov scored once on the power play and added an assist for the Thrashers (30-22-9), who also got a power-play goal from Steve McCarthy and an even-strength marker from Glen Metropolit.
Marian Hossa had two assists against his former team and Lehtonen finished with 25 saves as Atlanta lost its fourth straight game.
Hossa has eight points, all assists, in three games against the Senators this year. Kozlov, meanwhile, has seven points, including six goals.
Thrashers left-winger Brad Larsen left the game in the second period and didn't return because of a lower-body injury. His status was not immediately known.
Atlanta went 2-for-3 on the power play; Ottawa was 0-for-2.
The Thrashers came into the game having gone 1-5-1 in their past seven games, allowing Tampa Bay to creep within a point of the Southeast Division lead heading into Saturday's games.
Although Ottawa entered the game with a 15-5-2-4 all-time record against the Thrashers, Atlanta had already beaten the Senators in both previous meetings this season.
Gerber, making his second straight start with Ray Emery serving the second of a three-game suspension, was fresh off a 28-save shutout of the Florida Panthers on Wednesday.
McCarthy beat him through a screen with a shot from the point on the power play 11 minutes into the game to put the Thrashers ahead.
Schaefer scored on a rebound with 32 remaining in the period to even the score and Lehtonen had to be sharp to start the second, making a flurry of saves after Schaefer, Fisher and Alfredsson pinned Atlanta in its own end early on.
That allowed the Thrashers to retake the lead when Metropolit put a shot from close range past Gerber's shoulder.
Atlanta was on the power play less than three minutes later when Lehtonen gave up a big rebound on a shot from Antoine Vermette, allowing Kelly to score on the follow-up chance.
With Chris Phillips off for hooking, Kozlov snapped a shot between Gerber's pads from a bad angle to make it 3-2 after two periods.
Comrie scored on a rebound midway through the third to set the stage for McAmmond's heroics and Fisher capped things off with Lehtonen pulled in favour of the extra attacker.
Notes: The Senators scratched tough guy Brian McGrattan for the seventh straight game . . . Ottawa plays host to Edmonton on Tuesday . . . Emery is eligible to return Thursday versus Buffalo . . . Thrashers centre Steve Rucchin missed his fourth straight game with an upper-body injury. Left-winger Eric Boulton also didn't dress . . . Winger Denis Hamel faced the Senators for the first time since being claimed off waivers from Ottawa a week earlier . . . Atlanta wraps up its road trip Tuesday at Carolina.