Stewart's second goal of the game came as he crashed the net on a rush from the left wing, the puck wafting over the right shoulder of goalie Mathieu Garon and nearly knocking his water bottle to the ice.
Ian Cole had a goal and an assist and Alex Pietrangelo also scored for the Blues, who beat the Blue Jackets twice in 48 hours after losing their previous four games. Jaroslav Halak, returning after missing 11 games because of a cracked bone in his hand, made 19 saves.
Jake Voracek, R.J. Umberger and Derek MacKenzie scored for Columbus, which has dropped six in a row.
The game featured two teams struggling to remain in the Western Conference playoff chase.
The teams met just two nights hours earlier in St. Louis. It was a chippy, physical matchup, with two fights, big hits and three goals apiece by the teams in the opening period. The Blue ended up winning 5-4 in a shootout.
Down 3-1 coming into the third period, the Blues pulled even within 6½ minutes.
Cole, who had a goal waved off in the opening period, picked up his first career tally when his hard slap shot from the right side glanced off of Garon's shoulder and tumbled into the net.
Controlling the puck, the Blues squared things when Stewart scored on a tip off another hard Cole shot.
After a scoreless first period, the Blue Jackets reeled off three goals in the middle period in a span of 6:24.
On a pretty tic-tac-toe sequence, Rick Nash passed from the right boards to Derick Brassard at the left wing, with Brassard then saucering a pass to Voracek in the crease for his 14th of the year. Brassard had missed the last eight games with a bruised hand.
They made it 2-0 on the power play. Grant Clitsome's wrister from the left side was redirected by Umberger for his 21st of the season and his 50th point.
Then MacKenzie stepped into a one-timer from the high slot from Jared Boll that eluded Halak.
Late in the period, the Blues cut the gap to two goals on Pietrangelo's rocket from near the right hash marks.
Garon, playing for only the seventh time in Columbus' last 23 games, finished with 22 saves.
Cole had a goal waved off with 4 minutes left in the opening period. He flipped the puck at the goal cage from the back boards and it slipped past the right skate of Garon who had not sealed off the post. But the officials ruled the Blues' Cam Janssen had made contact with Garon and spun him slightly before Cole's shot.
NOTES: The game was the Blue Jackets' 400th at Nationwide Arena. They are 192-154-54. ... Blues C Alexander Steen sustained a lower-body injury in the second period. ... Stewart has three goals and two assists in a four-game points streak.