It was unclear whether Kompany would be back for Sunday's game against Estonia in Brussels. Belgium hasn't missed Kompany yet in its Group H qualifying campaign, scoring 13 goals and conceding none as it won its first three matches.
But his absence was felt as the Netherlands had the best of a scrappy first half, with Vincent Janssen twice getting in behind the Belgium defense - only to run into goalkeeper Simon Mignolet both times.
The two collisions took their toll on the unproductive Spurs striker and he was substituted in the 25th minute, pointing to his head as he left the pitch.
The Netherlands finally broke through when a long ball by Georginio Wijnaldum found Jeremain Lens. Jan Vertonghen, playing at the Amsterdam Arena for the first time since leaving Ajax for Spurs in 2012, grabbed Lens' shirt to bring him down.
Klaassen hammered the resulting penalty high into the roof of the net.
Ajax captain Davy Klaassen had given the Netherlands the lead from the penalty spot in the 38th minute as the neighbors played a friendly to prepare for their World Cup qualifiers on Sunday.
Belgium had been looking forward to the return from a string of injuries of captain Vincent Kompany (pictured), but the Manchester City defender pulled out of the starting lineup just before kickoff as a precaution.
The Netherlands was missing an injury-prone captain of its own, but Arjen Robben is fit and expected to play Sunday for his first international in a year when the Dutch take on Luxembourg in Group A.
Belgium started without a classic deep center forward, instead playing with a mobile front three of Eden Hazard, Dries Mertens and Carrasco. Their speed and positional switches caused problems for the Dutch defense, but they did not carve out any clear-cut chances before the break.
"We were well organized and didn't give much away," Netherlands captain Wesley Sneijder said. "But we didn't create much, either."
Belgium coach Roberto Martinez replaced Mertens with Lukaku in the 63rd and the powerful striker twice came close to levelling the scores 15 minutes later, first seeing a shot deflected wide and seconds later miscuing an effort from close range when he should have scored.
Instead it was Carrasco who finally made Belgium's pressure pay, with his shot deflecting off defender Joel Veltman and looping over Maarten Stekelenburg in the Dutch goal in the 82nd minute.
As Belgium poured forward looking for the winner, Lukako squandered another close-range chance and Stekelenburg saved well from Hazard to ensure the scores stayed level.
"The team played a good match," Carrasco said. "The second half we were going for goal."