Merzlikins made 21 saves in the first period, when Columbus took a 1-0 lead on Atkinson's goal at 14:49 with a shot from the high slot.
"You've got to give him credit," Devils coach Alain Nasreddine said. "It's not like our shots were from the outside. That's something we addressed. The guys were going to the net. We had scoring chances from dangerous areas, but he was sharp."
The Devils (17-24-7) have lost three straight entering the All-Star break and are 2-5-1 in the past eight games. Cory Schneider, in his first NHL start since Nov. 8 after spending two months with Binghamton of the American Hockey League, allowed four goals on 17 shots and was pulled in the second period.
"At that point, it was 4-0," Nasreddine said. "I was trying to change momentum. I'm not up here blaming Cory at all."
Mackenzie Blackwood, who returned after missing four games with an upper-body injury, made 13 saves in relief.
Atkinson extended the lead to 2-0 at 8:40 of the second period, 21 seconds after the Blue Jackets' second penalty kill of the period.