The Belgian-born youngster had the option to represent a number of countries including Belgium, Albania, Kosovo and England.
"I have received official confirmation that Adnan Januzaj has made himself available to the Belgium national team for the rest of his career," Wilmots tweeted.
There was no official comment from the Belgian Football Association or Januzaj himself.
England coach and former United defender Gary Neville added: "It's a personal choice and the boy has to be happy himself. You're talking about his own nationality, his own feelings, his own emotions and you always have to respect that."
Januzaj moved to Manchester United from Belgian side Anderlecht in 2011 and made his Premier League debut for United in the 2-0 win over Crystal Palace in September.
He made his first start for the club the following month and scored twice as United came from behind to beat Sunderland 2-1 at Old Trafford.
Later that month, the 19-year-old committed his future to United by signing a new five-year contract with the club.
Januzaj has made 13 Premier League starts for United, scoring four goals and assisting a further four.
It remains to be seen whether the youngster could feature at this summer's World Cup in Brazil.