The 30-year-old was named in Roberto Martinez’s starting XI for the game in Amsterdam - but after feeling some discomfort during the warm-up, he was replaced by Christian Kabasele.
It led to a flurry of speculation he had been injured, something Martinez was quick to play down in his post-match press conference.
"There is no injury," Martinez said. "We did not want to take any risks with him and Kompany did not feel well after the warm-up."
Kompany has battled back from a number of injury setbacks in the last two seasons and is gradually working his way towards full match fitness.
Belgium came from behind to draw the game, with Kevin De Bruyne playing 64 minutes before being replaced by Thorgan Hazard.