Thomas narrowly missed out on what would have been his fourth shutout this season as Bill Guerin banked the puck off a Bruins' skate just inside the final minute of regulation, but he held on for his 19th win of the year.
"They might be last in the East, but they're a good team," said Thomas of the Isles. "They're all NHL players and they tested us to our limit tonight."
Marc Savard and Martin St. Pierre got the goals for the Bruins, who have won eight of their last 10 games and lead the East with 70 points -- a full 42 points ahead of the Islanders, who are dead last in the conference with just 28 points through their first 44 games of the season.
Things aren't looking any easier going forward for New York, which lost incumbent starting goaltender Joey MacDonald in Tuesday's setback to the Rangers. MacDonald, who strained a groin muscle, joined franchise goaltender Rick DiPietro on the injury front.
"It was a good game," said Guerin. "We played hard, we played even with them or outplayed them, but a couple of bad breaks and it's in the back of our net."
Earlier on Thursday, the club agreed to terms with former backup goaltender Wade Dubielewicz on a one-way NHL contract for the remainder of the season.
Yann Danis took over for MacDonald on Tuesday and took the loss on Thursday, allowing both goals on 25 shots.
Danis held his own over the first 20 minutes denying the Bruins on each of their seven shots while Thomas withstood a 17-shot barrage from a desperate Islanders club.
Savard broke the scoreless deadlock, though, 3:30 into the second, skating with the puck out from behind the net toward the right circle and lighting the lamp with a sweeping shot that beat Danis to the far side.
Thomas continued to stonewall the Islanders, recording a dozen second-period saves and Boston took a two-goal lead early in the third.
Vladimir Sobotka fired a shot wide of the net and the puck caromed off the boards back in front where St. Pierre outhustled a pair of Isles defenders to swat the puck past a prone Danis at 6:51.
Guerin's fluke goal with 54 seconds remaining accounted for the final score, but Thomas needed to make one final save on a Chris Campoli blast after Danis was pulled.