The match kicks off at 9pm South African time.
Agadir has been built for the 2015 Africa Cup of Nations tournament, to be hosted by Morocco. The match against Bafana is the first time the stadium will be utilised.
It will also host four matches of the 2013 Fifa Club World Cup in December.
The multi-purpose stadium will mainly be used for football and will be home to local club Hassania Union Sportive of Agadir (HUSA), who have been using Stade Al Inbiaat, where Bafana Bafana trained on Wednesday afternoon.