Bakkali received a surprise first call-up for the friendly against France two weeks ago, just days after making his senior debut for PSV.
He later withdrew because of injury and has not played since, missing the Dutch club's Champions League tie against AC Milan.
Defenders Vincent Kompany and Thomas Vermaelen miss out due injury.
Belgium lead their World Cup qualifying group by three points from Croatia with three games left. Scotland have won just one match in seven and are out of contention.
(Reporting by Mark Gleeson in Cape Town, editing by Ed Osmond)
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