Ondrej Pavelec stopped 28 shots, losing a bid for his first career shutout on Chris Kelly's goal with 1:18 remaining in the third. The 21-year-old Pavelec was pulled in the first period of Friday's 7-3 loss to Boston after allowing three goals on four shots.
Slava Kozlov scored his 14th goal midway through the first, and Armstrong increased the lead to 3-0 when he beat Martin Gerber twice early in the third.
Todd White scored into an empty net for the Thrashers, who ended a 0-2-1 skid and won for just the third time in 14 games (3-9-2).
Gerber stopped 21 shots in his third start in four games. He had allowed one goal in his previous two outings, including a 24-save performance for his 10th career shutout in Ottawa's 2-0 win over Tampa Bay on Saturday.
The Senators have been held to four goals overall in their past four games. Ottawa's top line of Daniel Alfredsson, Dany Heatley and Jason Spezza has combined to produce just one point between them during the stretch.
Kozlov gave Atlanta a 1-0 lead on a power play midway through the first. A video review confirmed that the veteran left wing's deflection of Ron Hainsey's shot past Gerber 10:50 in did not make contact with the puck above the height of the crossbar.
Armstrong put Atlanta up 2-0 with his fifth goal 2:10 into the third period. He added his sixth of the season 31 seconds later to make it a three-goal lead, a franchise record for the fastest two goals by one player in a road game.
NOTES: Chosen 41st overall by Atlanta in the second round of the 2005 entry draft, Pavelec is 6-8-0 in 17 appearances with the Thrashers overall, including a 3-5-0 mark in 10 games this season. ... Jon Sim holds the Thrashers' record for fastest two goals. Sim scored 22 seconds apart against Carolina on Oct. 13, 2006. ... Armstrong broke a team record previously held by Kovalchuk for the fastest pair of goals by one player in a road game.