Stoner hit Thornton at center ice, near the San Jose bench. Thornton went to the Sharks dressing room at 11:25 of the first period and did not return to the game.
Coach Todd McLellan said Thornton wasn't seriously injured.
"[Thornton's] fine," McLellan said. "He'll be OK. … We've got a couple of days before we play again. I know [Thornton] pretty well. He won't be out very long."
Thornton's 33 points lead the Sharks. He had an assist on Joe Pavelski's goal at 4:33 of the first before the Stoner hit.
San Jose defeated Anaheim 3-0 to end a two-game skid.
Thornton has played in all 38 Sharks games this season.
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