Belgium coach Marc Wilmots tweeted on Monday that the Manchester City defender would miss Friday's Group A fixture in Croatia and the visit of Wales four days later.
Kompany was substituted 34 minutes into City's 3-1 Premier League win over Everton on Saturday.
Wilmots later told a news conference he had sought to call up 18-year-old midfielder Adnan Januzaj as a replacement.
Januzaj, who scored twice on his first league start for Manchester United in a 2-1 win at Sunderland on Saturday, was born in Brussels to Kosovar-Albanian parents and was on the books of Anderlecht before his move to the English champions.
Wilmots said United had told the Belgian FA that Januzaj had not chosen any national side and would not be joining up with the Belgium squad.
"But I think that I have given a clear signal to Januzaj. It's now up to him," Wilmots said. "I wanted to integrate him into the group, without forcing him. I respect his choice and plan to talk to him and his entourage."
Wilmots also said striker Christian Benteke would definitely not be fit for the Croatia clash, but might return for the home game against Wales.
Benteke picked up a hip injury in Aston Villa's 1-0 victory at Norwich on September 21. Villa initially said he would be out for at least four weeks.
Belgium top Group A with a five-point advantage over second-placed Croatia and a draw in Zagreb would mean they reach their first finals in 12 years.
Even if they lose to Croatia, Belgium would still ensure their ticket to Brazil in 2014 with victory in their last match against Wales.
(Reporting By Philip Blenkinsop; Editing by Alison Wildey and Sonia Oxley)
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