Magqwaka, 18, has been unable to train since straining a calf muscle on Tuesday, with Bafana set to face Congo in back-to-back Africa Cup of Nations qualifiers on October 11 and 15.
"We have advised Bafana that he is injured, he couldn’t train for the last few days," De Sa said after his team's 3-0 victory over Mpumalanga Black Aces in the Telkom Knockout on Sunday.
"He picked up an injury against Santos on Tuesday in a friendly and he tried to train a bit more but we had to pull him out because he has a very bad calf strain."
De Sa, though, says the decision on Magqwaka's availability for Bafana ultimately rests with the national side's medical team.
"Obviously if Safa wants him then he has to go but he’s nowhere ready to play and has to stay out for a couple of days and recover."