Ovechkin also had two assists. Nicklas Backstrom had a goal and three assists, Matt Bradley had two goals and an assist and Brooks Laich had two goals for the Capitals, who have won three of their last four games.
Washington goalie Cristobal Huet started and gave up two goals on 22 shots in two periods, but left the game with an apparent back injury. Olaf Kolzig played the third period and stopped all five shots he faced.
The win gives Washington 70 points, three behind Carolina for first place in the Southeast Division.
Ovechkin, who got his third hat trick this season, has 90 points and leads the league in scoring.
Marco Sturm and Dennis Wideman each had a goal for the Bruins, who had a six-game winning streak end.