According to the KickOff website, the pair had to be separated by team-mates and officials after punches were exchanged.
Smith confirmed the scuffle with McCarthy, 35, but insisted all is fine now.
“It was in the line of duty. It happens in football, but it was nothing serious,” he said.
McCarthy is not part of the Bafana Bafana squad for the current Africa Cup of Nations (AFCON) tournament being held in South Africa, but is expected to return to action with Pirates when the PSL season recommences on Tuesday, February 12.