Bafana coach Stuart Baxter is faced with a selection headache in midfield where he will be without at least two influential figures.
Zungu suffered a knee injury while on duty with his French club Amiens over the weekend, and was stretchered off the pitch after 59 minutes.
The 25-year-old centre-mid will not report for Bafana duty as he undergoes further tests to determine the extent of his injury.
Zwane and Kekana, meanwhile, both exited the field with knocks in Mamelodi Sundowns' MTN8 semi-final loss on penalties to Cape Town City at Lucas Moripe Stadium yesterday.
The Brazilians coach Pitso Mosimane had immediately raised doubts over their fitness for the national team, citing the nature of their injuries.
"'Mshishi' [Zwane] dislocated his toe and kept going and limping. It was a challenge," Mosimane said.
"Kekana had a knee injury and I had to make the substitution.
"These are two key players to win the match because they know how we play, and it's important to have them to win the match."
SAFA have since confirmed the withdrawal of Zungu and Zwane, while Kekana is still undergoing a late assessment at Chloorkop.
@BafanaBafana midfielders Bongani Zungu & Themba Zwane have been withdrawn from the squad due to injuries. Midfielder Hlompho Kekana is in serious doubt & undergoing tests at his club. Zwane was in camp but got left behind after a medical check up by the national team doctor— Bafana Bafana (@BafanaBafana) September 3, 2018