Zenit St Petersburg's Lombaerts has been struggling with a torn thigh muscle but would likely have played, especially given the absence of injured Belgium captain Vincent Kompany.
"Lombaerts will not be part of the official selections for the Euros. Christian Kabasele joins up with the squad this evening," Wilmots said in a tweet.
Lombaerts, aged 31 and with 39 caps, had played seven of Belgium's 10 qualifying matches for Euro 2016.
Wilmots also has concerns over another defender, Dedryck Boyata, who was injured in training on Monday.
Belgium, who have to confirm a 23-man squad by Tuesday's UEFA deadline, have included the uncapped Racing Genk defender Kabasele, 25, as a potential replacement.
Belgium play friendlies against Finland on Wednesday and Norway on Sunday before facing Italy in their Euro opener in France on June 13. Ireland and Sweden are also in Group E.
(Reporting by Philip Blenkinsop; editing by Ken Ferris)
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