The Canucks won their second straight and have five victories in six games. They crept within two points of Chicago for the best record in the Western Conference despite letting an early two-goal lead get away.
San Jose got goals from Logan Couture and Joe Thornton 5 minutes apart in the second to tie it.
Neither team could score again until Ebbett came through with his fourth goal of the season in extra time.
Roberto Luongo stopped 33 shots for the victory. He has won five of his last six starts.
Niemi made 27 saves.