Phungwayo suffered an Achilles injury in the MTN8 Final against Platinum Stars in Durban last weekend, and was replaced in the first half by Thabo Matlaba.
The former Bidvest Wits defender has undergone surgery and is only expected back in January next year.
Meanwhile, Bucs communication manager Mickey Modisane tells KickOff.com that Zambian striker Collins Mbesuma is back in full training, after recovering from a foot injury.
“He is back at training and working hard to improve his fitness,” Modisane says.
Pirates face Esperance in the CAF Champions League semi-final, first leg, on Saturday.