The third member of that line, Chris Kelly, registered a goal and an assist.
Joe Corvo and rookie Josh Hennessy, with his first in the NHL, also had goals for the Senators (23-19-2).
Ottawa provided plenty of offensive support for goaltender Martin Gerber, who was making a rare home start in place of Ray Emery.
Gerber stopped 20 shots and Wade Redden and Anton Volchenkov added a pair of assists as the Senators, in the midst of a five-game homestand, won for the sixth time in eight games.
R.J. Umberger scored the lone goal and Antero Niittymaki lost his 11th straight decision for the lowly Flyers (11-27-4). Niittymaki finished with 37 saves.
Philadelphia continued to unravel during its eight-game road trip. Sunday's loss was its third straight, including a 4-3 defeat at Boston on Saturday afternoon, after winning three in a row.
The last time Gerber started at Scotiabank Place was Nov. 13, when he was between the pipes for a 6-3 loss to Montreal. Since then, he's had to settle for road work and one relief appearance at home.
He hadn't appeared in any game in the Senators' past seven outings since beating the Flyers 6-3 on Dec. 23 at Philadelphia.
Niittymaki hadn't seen much action lately, either. He was playing for the first time since Dec. 27 after missing three games because of a hip problem and backing up Robert Esche for two more.
And the Flyers were once again with the services of Peter Forsberg, who continues to be sidelined by injury problems and missed his third straight game with a groin strain. They fell to 0-12-3 without their captain in the lineup this season.
The Senators were coming off a 3-2 loss to New Jersey a day earlier but the Flyers aren't about to be confused with the Devils.
Alfredsson made it 1-0 less than seven minutes into the game when Wade Redden's shot bounced off Flyers defenceman Alexandre Picard and fell to the Senators' captain, who was left unchecked at the side of a wide-open net for an easy tap-in.
Corvo made it 2-0 late in the period with a blast from the top of the faceoff circle.
Gerber didn't look sharp in allowing the Flyers to cut the lead to a goal early in the second, when his failed poke check in a race to a loose puck gave Umberger an empty net to shoot into, but Heatley restored the two-goal cushion on a breakaway midway through the period.
Hennessy, who was appearing in his eighth career game after being recalled from AHL Binghamton on Saturday because of a rash of injuries to Ottawa's centres, pounced on a rebound to record his first goal before the period was over.
Kelly rounded out the scoring with another drive from the faceoff circle in the third, where Philadelphia's Ben Eager livened things up by spearing Senators' tough guy Brian McGrattan.
Eager, an Ottawa native, received a five-minute major and game misconduct for his efforts.
Notes: The Senators are 17-8-7-0 against the Flyers since the 1998-99 season . . . Mike Fisher (knee), Jason Spezza (knee) and Antoine Vermette (hip) all sat out for Ottawa . . . Right-winger Stefan Ruzicka was scratched from Philadelphia's lineup . . . The Flyers conclude their road trip Tuesday night at Washington . . . The Senators are at home to Boston that same night.