Khudobin got his first shutout since late February and his fifth career. The Ducks have rebounded nicely following a 1-7-2 start.
Martin Jones made 16 saves and the Sharks lost to the Ducks for just the second time in their last seven meetings.
San Jose centre Tommy Wingels thought he tied it midway through the second period after he grabbed Hampus Lindholm's turnover and fired a shot that hit Khudobin's stick and clanked off the corner of the crossbar.
It was originally ruled a goal, but replays showed the puck did not cross the line. A review reversed the call.
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