Rich Peverley and Patrice Bergeron each had a goal and an assist and Chris Kelly also scored for the reigning Stanley Cup champions, who won for the second night in a row to move atop the Eastern Conference standings. Andrew Ference had two assists.
Boston, which went 3-7 in October, has 41 points and one more win than Philadelphia.
"We were behind the 8-ball there at the beginning of the season," Thomas said. "It was a tough start for us and tough overcoming that Stanley Cup hangover. We've definitely turned it around."
The Bruins have gone 17-2-1 since Nov. 1, when they launched a 10-game winning streak with a 5-3 win over Ottawa.
"To be honest, I didn't know that," said Kelly, who restored Boston's one-goal lead in the second. "I think that's maybe a good thing, that we're just playing every game. There are still points of our game that we can get better at and that's not necessarily a bad thing."
"They're a team that we know clogs it up in the neutral zone very well," Alfredsson said. "Unfortunately, we couldn't get as many goals as we would have liked on the chances we created in the first two periods."
Craig Anderson stopped 24 shots for Ottawa.
The Boston captain missed his second straight game after injuring his left knee Saturday in Columbus.
The Senators were without Milan Michalek, who sustained a concussion Tuesday night. Michalek was injured in a collision with teammate Erik Karlsson after scoring his NHL-leading 19th goal earlier in the game.
"I played junior with Nick and we're good friends," McQuaid said. "Obviously, when we play against each other we compete against one another, but I certainly would never intentionally try and do anything to hurt him or anyone else. I was just kind of pinching in and trying to keep the puck in and he made a kind of a quick move around me and I was just trying to do what I could to get in his way."
Foligno went to the dressing room but returned before the end of the second to take a shift during the ensuing power play.
"I think Adam was just trying to stop me from getting around him and I don't think he realized his knee was out that far, and he clipped me," Foligno said. "I think it looks worse than it was. It was bad but it got me on the leg so I'm happy at least it wasn't on my knee. My quad's got a charley horse but that's about it."
Thomas stopped each of the 13 shots he faced in the opening period as Boston took a 1-0 lead 12:10 in on Peverley's second goal in two nights.
Peverley assisted on former Senators center Kelly's goal 13:47 into the second to put the Bruins up 2-1. Kelly got behind defensemen Matt Carkner and rookie David Rundblad and was all alone to put a rebound of Johnny Boychuk's shot between Anderson's pads.
Bergeron made it 3-1 with an unassisted effort 4:54 into the third. The Bruins center took advantage of Alfredsson's uncharacteristic turnover at the Ottawa blue line and drove in to beat Anderson with a deke for his sixth goal.
Paille beat Anderson on a breakaway at 5:50 to increase the lead to 4-1. He added his second of the game with 1:04 remaining after Spezza scored at 15:55.
Spezza assisted on Alfredsson's goal 4:23 into the second that tied it at 1.
- Bruins LW Milan Lucic fought with Carkner in the first.
- Boston is 6-5-3 without Chara in the lineup since 2006, when he left the Senators to sign with the Bruins as a free agent.
- Alfredsson's goal was the 397th of his career.
- Spezza has a goal and six assists during a four-game points streak.