The defender had several chances to add his name to the scoresheet, and was mere inches from opening the scoring after 23 minutes when he flung himself at a corner and was unlucky to see the ball fly narrowly over the bar.
Romelu Lukaku put Belgium in front in the first half, and Eden Hazard found the net in stunning style in the second, exchanging quick passes with Origi before making space at the edge of the box and firing past the despairing Isaksson.
Kompany marshalled a defence that never really looked in danger of conceding to a Sweden missing Zlatan Ibrahimovic, who was only fit enough for the bench.
Belgium continue their warm up for Brazil with a friendly against Tunisia on Saturday.
Elsewhere, Aleks Kolarov chalked up another 90 minutes for Serbia in a 1-1 draw with Panama. The defender is a key figure for his country and bagged himself a goal in the previous clash with Jamaica, but compatriot Matija Nastasic was not called up for this series of friendlies after an injury-hit season.
Serbia failed to qualify for the World Cup, but have an opportunity to face hosts Brazil in a friendly in São Paulo on Thursday.
