Thornton scored in the first period, and Patrick Marleau had a shorthanded goal in the second for the Sharks (38-24-6), who swept the two-game season series with the Capitals. Brent Burns scored his 25th goal into an empty net with 43.2 seconds left, and Martin Jones made 23 saves for his 34th victory.
"I think obviously everybody knows the Washington Capitals are having a great year and are a great team," Marleau said. "You don't want to get embarrassed in those games, you want to show your best, and I think the boys did a good job tonight."
The Sharks are three points behind the Los Angeles Kings for first place in the Pacific Division and one point behind the second-place Anaheim Ducks.
T.J. Oshie and Justin Williams scored in the second period for Washington (49-14-5), which would have become the first NHL team to clinch a Stanley Cup Playoff berth with a victory.
"They had all the energy and all the jump," Capitals coach Barry Trotz said of the Sharks. "Everyone we're playing is in playoff mode, fighting for position. They are marking us, using us as a yardstick because of our record. So every game is hard. You have to fight for inches."