Kompany was named in Roberto Martinez's starting line-up for the friendly match, on his return to the national squad, but following the pre-match warm-up the central defender was replaced by Watford's Christian Kabasele.
Local media reports said the 30-year-old felt some discomfort and was withdrawn as a precaution but it is yet another concern for the player himself and City boss Pep Guardiola.
A series of injuries have limited Kompany to only four appearances this season and he played only 14 Premier League matches last season
The game itself saw Kompany's team-mates come from a goal down to draw, with Yannick Carrasco equalising late on to cancel out Davy Klaassen's first-half penalty
Both managers fielded strong sides with Chelsea's Eden Hazard the captain for Belgium while Tottenham's Jan Vertonghen and Kompany's City colleague Kevin De Bruyne were also picked
For Holland, Vincent Janssen, Maarten Stekelenburg, Virgil Van Dijk, Daley Blind and Gini Wijnaldum were among the Premier League stars on show
Belgium started the brighter but the first real chance came Holland's way after a defensive mistake from Laurent Ciman
His header back towards Simon Mignolet was weak, allowing Janssen to steal in and knock the ball past the Liverpool goalkeeper, but Ciman just about made amends and recovered
The visitors were getting plenty of balls into the penalty area but more often than not Van Dijk was there to head them away or avert the danger
Janssen gave Tottenham some injury concern when he went off after 25 minutes following a clash with Mignolet
Dries Mertens should have put Belgium in front with the very next attack but he headed De Bruyne's cross into the side netting
Holland had been on the back foot throughout but took the lead seven minutes before half-time
It was poor defending from Vertonghen, who let Jeremain Lens get the wrong side of him at the byline before pulling him back by the shirt
It was a definite penalty and Ajax striker Klaassen dispatched it with aplomb, straight down the middle, for his third goal for the Oranje and on his home ground
Belgium felt they should have had a penalty after an hour when Joel Veltman dragged back Carrasco from behind but the referee awarded just a free-kick
De Bruyne took the set-piece and his shot had to be helped over the crossbar by Stekelenburg
Martinez's men had struggled to really get going and he made a double change four minutes later, bringing on Thorgan Hazard and Romelu Lukaku for De Bruyne and Mertens
Belgium survived a scare when Joshua Brenet's shot curled narrowly wide but they improved immediately with Lukaku sending an effort just wide before the Everton striker was guilty of a glaring miss after 79 minutes
Thorgan Hazard sent a shot across the face of goal and Lukaku, unmarked with an open goal inside the six-yard box, could not sort his feet out in time and scooped the ball over the crossbar
Belgium finally made the breakthrough with eight minutes left when Carrasco's shot deflected off the back of Veltman and over the head of Stekelenburg.
Eden Hazard could have won it for the visitors in the 86th minute when Lukaku's flick put him through one-on-one with Stekelenburg but the Everton goalkeeper made a good save.
Both countries move on to World Cup qualifying matches this weekend with Holland travelling to Luxembourg while Belgium host Estonia in Brussels
Source : PA
Source: PA