Kirill Kaprizov scored his 30th goal of the season, Mats Zuccarello had a goal and an assist, and Kaapo Kahkonen made 26 saves for Minnesota (34-19-4), which had won two straight, including a 6-5 shootout victory at the Detroit Red Wings on Thursday.
"They kept pushing and got a break at the end," Wild coach Dean Evason said. "We make a mistake and it ends up in our net."
Chinakhov gave the Blue Jackets a 1-0 lead at 13:31 with his first NHL power-play goal, scoring from the top of the left face-off circle.
"When he really figures this league out, it's going to be scary for other teams," Werenski said of Chinakhov, who has played 48 games in his first NHL season.
Kaprizov tied it 1-1 at 19:34 on a 4-on-3 power play with a wrist shot from the left circle. He has scored 11 points (seven goals, four assists) in an eight-game point streak.
Zuccarello gave the Wild a 2-1 lead at 13:33 of the second period from between the circles when he redirected a Jared Spurgeon shot. Merzlikins got a piece of the puck but it trickled behind him.
"It's tougher to accept the loss when you feel like you should've won and you played good," Zuccarello said.
Merzlikins made 11 saves in the third period and five in overtime. He lost his previous three starts.
"I got tired of working my [butt] off and not getting the results I want," Merzlikins said. "I just thought, I'm not going to think anymore. I'm just going to go out, play hockey and have fun."