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.
"Manchester United told me that Januzaj has not made a decision to play for a national team yet, not for any country," Wilmots said.
"We gave a clear signal [that we want him to play for Belgium] and now it's up to him. I will respect his choice."
"But I think that I have given a clear signal to Januzaj. It's now up to him.
"I wanted to integrate him into the group, without forcing him. I respect his choice and plan to talk to him and his entourage."
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.