Petr Tenkrat and Brandon Bochenski also scored for the Bruins, who snapped a three-game losing streak and moved six points behind eighth-place Carolina in a crowded race for the Eastern Conference's final playoff spot.
Sheldon Souray scored his 23rd goal for Montreal, which lost its third straight and fourth in five to remain one point behind the Hurricanes.
Jaroslav Halak made 33 saves for Montreal in his sixth career start after being called up from Hamilton of the AHL on Feb. 14. Starting goaltender Cristobal Huet is out for the rest of the regular season with a left hamstring injury.
Thomas was tested often in the final period, making a pair of stops on Tomas Plekanec and Andrei Kastsitsyn seconds apart with just under 12 minutes left.
Murray's goal, a wrister from the slot, made it 3-1 with 4:09 to play
Two nights ago, Bruins coach Dave Lewis was frustrated after his team gave up 55 shots on goal in an overtime loss to the Flyers, calling the performance "totally ridiculous."
On Saturday, the Bruins controlled play for extended periods before grabbing a 1-0 lead on Tenkrat's goal 3:30 into the second.
Tenkrat fired a slap shot from just outside the right circle and the puck caromed off the stick of defenceman Souray, knuckling over the right shoulder of Halak.
Bochenski made it 2-0 with 1:03 left in the second. He collected a loose puck at centre ice, broke in down the left wing and slipped a wrister inside the left post.
Souray's shot ricocheted off defenceman Andrew Ference's stick and past Thomas 3:02 into the third period.
The best chance of a scoreless first period came when Halak made a nice left pad save with 3:16 left on Shean Donovan, who broke in alone from the right wing.
Halak also stopped three booming slap shots from the point by Zdeno Chara in the final minute while the Bruins were on a power play.
Notes: Thomas was coming off a career-best 51-save performance in the 4-3 overtime loss to the Flyers Thursday. ... A large contingent of Canadiens fans, filling a good portion of the east end of the building, broke into chants of 'Go Habs Go' numerous times. ... Montreal played the third of five games in 12 days away from home, and travels to Atlanta and St. Louis before returning home against the Islanders on March 13.