Fantilli scored from the slot off a pass from Kent Johnson. The goal came after Jackson LaCombe tied it 3-3 with 3:16 remaining in the third period for Anaheim with a shot from below the goal line that went off the mask of Jet Greaves.
Boone Jenner had a goal and an assist, and Greaves made 25 saves for the Blue Jackets (14-13-6), who were 0-4-1 during their losing streak.
Mikael Granlund had a goal and an assist, and Ryan Strome also scored for the Ducks (20-12-2), who were coming off a 4-1 win at the New York Rangers on Monday and finished a five-game road trip 2-2-1. Ryan Poehling had two assists, and Ville Husso made 24 saves.
Werenski gave Columbus a 1-0 lead at 8:21 of the first period on a wrist shot off a feed from Jenner.
Strome tied it 1-1 at 3:35 of the second period from the slot after a backhanded pass from Poehling.
The Blue Jackets went up 3-1 on goals 19 seconds apart by Werenski at 3:59 and Jenner at 4:18.
Werenski scored on the rush from the right circle for his second goal of the game. Jenner then put in his own rebound after tipping a shot by Ivan Provorov.
Granlund cut it to 3-2 at 5:29 with a wrist shot from the left circle.