Radja Nainggolan scored the only goal in the 84th minute to hand his side a victory which sees them finish Group E on six points.
That sets up a clash with Group F winners Hungary in the Round of 16 in a match which will take place on Sunday afternoon.
Belgium needed at least a draw to qualify automatically and Head Coach Marc Wilmots only made one change to the team which emphatically defeated Ireland 3-0 last time out, bringing in Nainggolan.
That meant De Bruyne kept his place in the side after an impressive showing against Martin O’Neil’s side where he assisted the opening goal, while City’s Jason Denayer was on the bench.
Kevin looked a lively presence from the start for the Red Devils and forced former City goalkeeper Andreas Isaksson into a good save on 24 minutes with a curling, dipping strike from outside the area.
He was at it again five minutes later when he beat his marker and drove the ball across the face of goal invitingly but Romelu Lukaku wasn’t up with play and able to touch it in.
If there was going to be an opening goal in the first half, it looked as though it was going to come via a De Bruyne assist but Sweden held out until the interval as they sought to keep their slim qualification hopes alive.
De Bruyne forced Isaksson into an even better save after 65 minutes when he drilled in a searing strike with the outside of his foot with the goalkeeper required to tip the ball around the post at his near post.
The pressure was ratcheting up from Wilmots’ men but Sweden carried their own threat on the counter spearheaded by Zlatan Ibrahimovic who was potentially playing his final international game.
Ibrahimovic had the ball in the back of the net on 67 minutes but the “goal” was ruled out due to a foul in the build-up to the chance.
Just when it looked as though Belgium were going to limp over the line to qualify with a goalless draw, Nainggolan came up with something very special indeed – a stunning long range volley which rocketed past Isaksson and gave his side the win.
Next up: Belgium will take on Hungary on Sunday evening in Toulouse in the Last 16, while the Republic of Ireland will meet France after they also qualified thanks to their surprise 1-0 victory over Italy.
