"We got through it without injuries," Blue Jackets coach John Tortorella said. "That's the most important thing."
Columbus (47-31-4), which won seven of its final eight games, will play the Tampa Bay Lightning, who won the Presidents' Trophy, in the first round of the playoffs. The Blue Jackets finished one point behind the Carolina Hurricanes for the first wild card.
Pierre-Luc Dubois scored twice, Oliver Bjorkstrand had a goal and two assists, and Joonas Korpisalo made 27 saves.
"We always want to finish on a good note. Just get into our game, feel good about your game going into the playoffs," Blue Jackets captain Nick Foligno said. "I thought, for the most part, we did that. It's obviously a tricky game with not much at stake, but we did a lot of the good things and found a way to get a big win on the road and take that into the playoffs."
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Thomas Chabot and Mikkel Boedker scored for Ottawa (29-47-6), which lost three of its final four games. Craig Anderson allowed three goals on seven shots before being pulled in the first period. He was replaced by Anders Nilsson, who made 17 saves.
"Obviously, we didn't help [Anderson] at all," Chabot said. "Most of the goals that got scored, there's nothing really he could do."
Dubois scored short side from low in the left circle to give the Blue Jackets a 1-0 lead at 3:39 of the first period.
Bjorkstrand deked Senators defenseman Mark Borowiecki at the point before sending a cross-ice pass to Markus Nutivaara, who scored with a one-timer to make it 2-0 at 9:08.