The Senators, who scored three short-handed goals, can clinch a playoff spot Friday night when they close out the regular season at home to Boston.
"I didn't like the hit," Murray said. "The knee came out, and it was a hit to the head."
Leafs coach Paul Maurice said: "It was a good hit. It was clean."
The hit on Alfredsson seemed to spark the Senators, who were ahead 2-1 late in the first period when he was flattened.
"That definitely got us going," said Dany Heatley, who scored twice. "That's our captain."
Murray said Alfredsson had "a bit of a knee problem" and an upper body injury and almost surely won't play in Friday's regular-season finale at home to Boston. The question is, will Alfredsson be back in time for the first round of the playoffs next week? The team was expected to provide another update on Alfredsson on Friday.
The Senators also lost center Mike Fisher to a knee injury early in the first period.
A loss on Thursday night would have left the slumping Senators scrambling to get into the postseason. But the win kept Ottawa in sixth place in the Eastern Conference at 94 points, three ahead of ninth-place Philadelphia. Boston and Washington occupy the last two playoff spots at 92 points.
Bell and Dominic Moore scored for the Leafs, who fittingly ended their home schedule with a beating in their third consecutive season outside of the playoffs.
Bell opened the scoring at 6:30 of the first period. But that's when the fun stopped for Leaf fans.
"We gave up the first goal tonight which is always a concern given the way we've played lately," Murray said. "But we held together. The guys were great on the bench. We stuck with it."
Ottawa tied it on Heatley's one-timer on a power play at 11:12.
The Senators took the lead 2-1 with 2:45 to go in the first when Alfredsson picked up his second assist with a nice feed to Spezza on a 3-on-1.
The game took a nasty turn on the next shift when Bell nailed Alfredsson -- who had his head down -- with a check that drilled the Senators' captain to the ice. He was slow to get up and the Ottawa bench was livid, but there was no penalty.
Vermette scored a pair of rebound goals in the second making it 5-1 after 40 minutes.
McAmmond and Vermette scored short-handed goals in the third. Vermette put in his own rebound at 3:11 after Toskala stopped his first two attempts for No. 23 on the season.
- Veteran winger Cory Stillman returned to the Ottawa lineup after missing two games with a leg injury.
- The Leafs were once again without top scorers Mats Sundin (groin) and Nik Antropov (knee). The Leafs close out their regular season Saturday night at Montreal with backup G Andrew Raycroft in net.
- It was the third time in franchise history the Sens scored three short-handed goals in a game.