Emil Bemstrom and Eric Robinson scored for Columbus (33-22-15).
Elias Pettersson replied for the Canucks (35-27-6) a week after failing to defend a third-period road lead against the Blue Jackets.
Columbus had just 22 shots on Canucks netminder Thatcher Demko, after recording 46 shots in their 4-1 loss to the Edmonton Oilers on Saturday night.
The Blue Jackets were 0 for 2 on the power play and Vancovuer could not score on its three man advantages.
With the win, Columbus moves into the first wild-card spot in the Eastern Conference with 81 points, two ahead of the Carolina Hurricanes and New York Islanders.
The Canucks remain tied with the Predators and Jets at 76 points, but Vancouver holds the second wild-card spot with one more win than Nashville and a game in hand over Winnipeg.
Following a sluggish first period that saw Vancouver outshoot Columbus 6-3, the Blue Jackets opened the scoring 7:18 into the second.
Pierre-Luc Dubois outmuscled Alex Edler for a loose puck along the end boards, then fed the puck to the slot. A wide-open Bemstrom beat Demko to the stick side for his ninth goal of the season.
With five minutes left to play in the second, Tyler Toffoli got Vancouver’s best chance to that point in the game, skating into the offensive zone with plenty of open ice. Merzlikins got a piece of Toffoli’s shot before it deflected off the goal post.
Robinson extended the lead to 2-0 on the Blue Jackets’ 10th shot of the game, beating Demko with a slap shot for his seventh goal of the year with 28 seconds left in the middle period.
The Canucks finally solved Merzlikins on their 21st shot of the night, when Pettersson burst out of the penalty box after serving an elbowing minor and slid the puck five-hole for his 27th of the season at 8:19.
The loss gives Vancouver a 1-2-0 record on its current homestand, which wraps up on Tuesday against the New York Islanders.
NOTES: Ryan Murray returned to the Columbus lineup after missing Saturday’s game in Edmonton â€¦ Brock Boeser skated with the Canucks on Sunday morning for the first time since suffering a rib cartilage injury on Feb. 8. His return date remains unknown â€¦ The Canucks celebrated Minor Hockey Night on Sunday.