Januzaj has featured in every squad, including for last year's World Cup, since deciding to play international football for Belgium last April. The 20-year-old had previously been courted by Albania and Kosovo.
"I have no doubts at all about his quality, it's just that there's little chance to see him, for him to show that quality," Wilmots told a news conference on Friday.
"In that position, there's incredible competition and at a certain point I have to say he's simply not playing enough at the moment."
Michy Batshuayi earned a first call-up. The 21-year-old Olympique de Marseille striker committed himself a year ago to Belgium over the Democratic Republic of Congo.
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Wilmots said he had been unable to pick Barcelona's Thomas Vermaelen and Everton's Kevin Mirallas due to injury.
Belgium play Cyprus in a Group B qualifier in Brussels on March 28 and travel to Israel for a game on March 31. Israel top the group after three wins from three matches.
Belgium, fourth in FIFA's world rankings, are fourth in Group B after a win and two draws, with Cyprus a point ahead of them in third.
Squad:
Goalkeepers: Thibaut Courtois (Chelsea), Simon Mignolet (Liverpool), Jean-Francois Gillet (Torino)
Defenders: Toby Alderweireld (Southampton), Laurent Ciman (Standard Liege), Laurens De Bock (Club Bruges), Jason Denayer (Glasgow Celtic), Vincent Kompany (Manchester City), Nicolas Lombaerts (Zenit St Petersburg), Thomas Meunier (Club Bruges), Jan Vertonghen (Tottenham Hotspur)
Midfielders: Nacer Chadli (Tottenham Hotspur), Kevin De Bruyne (VfL Wolfsburg), Steven Defour (Anderlecht) Moussa Dembele (Tottenham Hotspur), Marouane Fellaini (Manchester United), Radja Nainggolan (AS Roma), Axel Witsel (Zenit St Petersburg)
Forwards: Michy Batashuayi (Marseille), Christian Benteke (Aston Villa), Eden Hazard (Chelsea), Yannick Ferreira-Carrasco (AS Monaco) Romelu Lukaku (Everton), Dries Mertens (Napoli), Divock Origi (Lille)
(Reporting by Philip Blenkinsop, editing by Ed Osmond)
