Patrice Bergeron and Charlie Coyle scored for the Bruins (22-4-1), who went 2-1-0 on a three-game road trip. Linus Ullmark made 30 saves.
"A point of ours, we want to win every series against teams we played," Boston coach Jim Montgomery said. "It's funny. Vegas is a really good team and well coached. They're a real good first period team. We fell behind 1-0. That was a big point of emphasis for us, but we knew 1-1 in the third period, we knew we were the best team in the third period in the League."
Mark Stone scored, and Thompson made 24 saves for the Golden Knights (20-9-1), who finished 1-2-0 on a three-game homestand. They were without forward Jack Eichel, who missed the game because of a lower-body injury.
It was the third time in the past four games, including two against the Bruins, that Eichel was unavailable. Vegas won 4-3 in a shootout at Boston on Dec. 5.
"We were good. We were fine," Golden Knights coach Bruce Cassidy said. "They made the play when they had the opportunity, we didn't, they get the two points. Our guys can feel good about their effort and compete against a good hockey club, but when you lose, there are no moral victories in that regard."