"Timmy was our best player," Boston coach Claude Juilen said. "He held the fort."
Thomas was on the verge of his fourth shutout of the season, but Bill Guerin swept in a rebound with 53.2 seconds left. The puck deflected off Boston center David Krejci's skate.
"I saw it hit his skate," Thomas said. "I lost sight of the puck, and the next thing I see, their hands are in the air."
With the victory, the Bruins moved a point ahead of San Jose for the overall NHL lead. The Sharks faced Calgary at home later Thursday night.
"There are about six reasons why this team is different from previous Bruin teams," Thomas said. "One of the biggest things is that we're all on the same pages as the coaches are."
Yann Danis stopped 25 shots for the Islanders, losers of six straight. They haven't won in January, and have just two wins since the end of November.
"I felt a lot better as the game went on," Danis said. "I would like to have the first one back, but I'm not going to dwell on that."
The first period was scoreless, with New York outshooting the Bruins 17-7. Boston had the first shot on Danis, and then the Islanders took the next 12 against Thomas.
New York forward Kyle Okposo left the ice with assistance with about 4½ minutes left in the period after getting hit in the head with the puck. He returned during the second period wearing a plastic shield on his helmet.
The Bruins took the lead at 3:30 of the second period on their ninth shot. Savard, standing behind the net, came out to Danis' left and fired a quick wrist shot.
"I had some room to come out from behind the net," Savard said, "and I was just trying to get the puck on net."
Boston increased the lead in the final period when St. Pierre rapped in a rebound at 6:51 just after a power play expired.
Islanders coach Scott Gordon was pleased with his team's effort.
"We just played two teams in first place," Gordon said about the game and Tuesday's 2-1 loss to the Rangers. "We've started to put together more consistent 60-minute efforts. Obviously, it's only two games, but it's a very encouraging sign."
Notes: The Islanders signed former backup goalie Wade Dubielewicz from Russia, but he must secure his release before he can join the team. In the interim, the team called up Peter Mannino from Bridgeport to back up Danis.
