Washington appeared in command after going up 3-0 in the second period against Thomas, who came in 7-0 with a sparkling 0.72 goals-against average. Thomas already had two wins over the Capitals and had not given up more than two goals in a game.
But he was unceremoniously benched after the second period by coach Claude Julien, who was looking to inject a spark into the listless Bruins.
"Let's put it that way: It had nothing to do with Tim, OK?" Julien said.
"I understand," Thomas said. "Coach came and talked to me after the second period and told me what his thoughts were. And I said I understand and I agree."
Tuukka Rask replaced Thomas and kept the Capitals at bay while the Bruins scored three times in a 7-minute span of the third period to pull even. Michael Ryder started the run by tapping in a rebound with 16:53 remaining. Fifty-five seconds later, Nathan Horton scored his team-high sixth goal to get Boston to 3-2.
Shawn Thornton then put a backhander into the net with 10:09 remaining to chase the 22-year-old Neuvirth, who yielded three goals on five shots during the third period.
"He might be a little tired. He's not used to playing under this kind of pressure," Capitals coach Bruce Boudreau.
Neuvirth was replaced by Braden Holtby, who stopped Boston's final four shots to win in his NHL debut.
"I didn't know if it was fair to Braden to put him in his first game, 10 minutes to go against Boston in a tie, but he did outstanding," Boudreau said.
"Unfortunately, one 20-minute period is not good enough," Rask said. "We played a good period, battled back and I knew I had to shut them out. But they got one by me and that's enough."
Boston had won a franchise-record five straight road games to start the season and had defeated the Capitals 3-1 and 4-1 behind Thomas last month.
Washington defenseman Mike Green didn't play in that home-and-home series, however, and in this one he had a goal and an assist.
"It was important that we got pucks on net on him and created chances," Green said. "When we did get opportunities to shoot the puck like we can, we were putting them in. We were fortunate enough to get him taken out of net."
The Capitals went up 1-0 in the opening minute of the period when Sloan gained possession of the puck after a faceoff and sent a blast from atop the right circle past the screened Thomas. It was Sloan's fourth goal in 75 career games and first since Nov. 6, 2009.
Green added to the margin at 7:35. After taking a centering pass from Ovechkin, Green faked a shot, lined himself up between the circles and fired a wrist shot into the back of the net.
Then, during a Boston power play, Semin wrestled the puck away from Patrice Bergeron near center ice and passed it to Green, who pushed it back to Semin on the left side. Semin lifted a shot past Thomas for a 3-0 lead.
Washington outshot Boston 8-3 during a scoreless first period. The Capitals had a two-man advantage for 58 seconds but got off only one shot.
Thornton played in his 300th career game. ... Ovechkin extended his points streak to five games (4 goals, 5 assists). ... Washington outshot Boston 39-18.