Phungwayo, 29, and his brother Phelelani Aubrey Phungwayo, were at a party in Spruitview, East of Johannesburg, during the weekend when they were involved in an altercation with another man.
The man was allegedly assaulted and he was shot at. The bullet hit his ring finger.
The Pirates' left-back and his brother were arrested on Monday, but police failed to find the firearm that was allegedly used in the incident.
On Tuesday Magistrate Van Der Hoevel granted the brothers bail of R2 000 each. The matter was postponed to 23 June for further investigations.