National team manager Marc Wilmots confirmed via his personal Twitter account that Zenit St Petersburg defender Lombaerts would be replaced by the uncapped Christian Kabasele of Racing Genk.
The 31-year-old was included in the provisional 24-man selection, with Wilmots having to narrow his squad down to 23 by midnight on Tuesday, but has struggled to regain fitness from a torn thigh muscle.
Having played in seven of their 10 qualifying matches, Lombaerts was a potential candidate to come into the starting eleven in place of injured captain Vincent Kompany who will not travel to France with an injury that could keep him out for four months.
But Wilmots will no longer be able to call upon the defender, who has been capped a total of 39 times, having failed to return in time.
Otherwise, Celtic centre-back Dedryck Boyata has also been withdrawn after sustaining a muscle injury whilst making a sliding tackle in an open training session on Monday.
The player was immediately sent for scans and it is feared that he has suffered a muscle tear, Wilmots admitting that he thinks he suffered "a severe injury in training" and that he doesn't "think he will be ready" to play this summer.
Red Devils lose two more defenders as injuries begin to rack up
"I am no doctor but we believe it's a recurrence of his hamstring tear and we can put a cross next to his name," he added, suggesting it is "very bad" for Boyata, who has been capped twice, and he could be out "for six weeks."
No word has yet been given on whether Boyata will be replaced, but the Belgium boss remains confident in his options without the pair as he insisted: "I have a defence with Toby Alderweireld, Jason Denayer, Thomas Vermaelen and Jan Vertonghen. It's not too bad after all."
In his side's first friendly prior to the Euros, Wilmots experimented with a central defensive partnership of Vermaelen and Alderweireld, with Vertonghen at left-back and central midfielder Axel Witsel at right-back - before bringing on Jordan Lukaku to replace Vertonghen at half-time and later introducing natural right-back Laurent Ciman as he switched to a system with three central defenders.
Lombaerts and Boyata follow Club Brugge's Björn Engels in dropping out of the squad, with the 21-year-old recently ruled out because of a groin injury sustained towards the end of the club season.
Problems at the back are beginning to mount up for the Red Devils, with Thomas Meunier still short of full fitness and Vermaelen having played sporadically for La Liga champions Barcelona throughout the 2015-16 campaign.
Belgium are also sweating on the fitness of midfielders Mousa Dembele and Radja Nainggolan from a muscle tear and a calf injury respectively, although Wilmots insisted he was confident both could recover in time to be taken to the Euros.
Wilmots' side - ranked second in the FIFA World Rankings going into the tournament - will continue training in Genk before facing Finland and Norway at the King Baudouin Stadium in Brussels for their final two warm-up matches.
Roma's Nainggolan could be involved on the Sunday against Norway, as could the returning Yannick Carrasco after he joined up with his international teammates having played and scored in the UEFA Champions League final for Atletico Madrid, unfortunately losing 5-4 on penalties to rivals Real Madrid.
The Belgians fly to France on June 7 where they will face Italy, Republic of Ireland and Sweden in Group E of the Euros - their first fixture against the Italians on June 13 in Lyon.