Sonny Milano scored, and Elvis Merzlikins made 30 saves for Columbus (21-16-8), which had been 6-0-3 in its past nine road games.
"We weren't sharp out there," Blue Jackets coach John Tortorella said. "We didn't sustain any consistent forechecking. My concern right now is the start of every period, it's an epidemic."
Joe Thornton gave the Sharks a 2-0 lead at 13:28 of the second period with a slap shot from the top of the left circle nine seconds into a power play.
"He surprises me every night with something else," Boughner said. "I've increased his minutes and he's responded positively to that. I think he's been on a little bit of a resurgence on our power play, he's almost the catalyst, the quarterback."
Milano cut the lead to 2-1 with his fifth goal at 18:12, but Brent Burns made it 3-1 at 2:09 of the third period.