Curtis Lazar and Erik Haula scored, and Linus Ullmark made 28 saves for the Bruins (45-22-5), who have lost two of three. Boston fell one point behind the Tampa Bay Lightning for third in the Atlantic Division after Tampa Bay won 5-0 against the Buffalo Sabres later Sunday.
"The League is tightening up and we're getting to play for keeps here, so every game is a learning curve and I think as a whole we just need to expect a little bit more of ourselves and continue to improve and build," Lazar said.
Eller gave the Capitals a 3-2 lead at 7:18 of the third period when his attempted centering pass deflected off Haula's skate and past Ullmark.
"Tough bounce," Haula said. "It was just kind of the story in the third. I think they were the better team in the third and that was the difference in the game. It was a pretty even game, I thought, overall. But then (in the third) they had the better chances."
Trent Frederic appeared to give the Bruins a 1-0 lead at 7:01 of the first, but the goal was overturned after a video review confirmed that Frederic kicked the puck into Washington's net.
Carlson then put the Capitals ahead 1-0 at 4:11 of the second with his third goal in three games, a slap shot over Ullmark's glove from the top of the right circle.
"We don't have any room to lay off the gas," Carlson said. "We're in a tight race. We know that if we played like we were down the stretch here, our season's going to be really short."
The Bruins tied it 1-1 at 7:55 when Nick Foligno skated around Vanecek and found Lazar for the tip in.
"[Folgino] deked out the goalie and I was just trying to read if he was trying to go around the far side or get it back to the short side," Lazar said. "My favorite place to be is in that blue paint and I was able to whack it in and it was a big goal for us."