England, trailing 20-6 early in the second half, capitalised when the Boks were without Victor Matfield, who was yellow carded for pulling down a driving maul from a lineout.
The hosts scored two tries from driving mauls during that period to level matters. However, the second try came after a mistake from the assistant referee, who wrongly determined Bryan Habana had carried the ball in touch, with replays clearly showing the Bok wing's foot was grounded. What should have been a Springbok lineout inside England territory, turned into an attacking lineout for the home side within striking range, from which they eventually scored.
The Springboks managed to regain their composure to eke out a win, but Mallett was nevertheless critical of some of the decisions made by the officials.
Speaking in the SuperSport studio afterwards, Mallett said:
"Steve Walsh made a decision that had a really important affect on the game. He did warn both captains that the next person to transgress at the rolling maul would be off. So off goes Victor Matfield and England score two tries in five minutes. Walsh brought England completely back into the game.
"There always seems to be some controversy around Walsh. Even though he did warn the players and we should've been more careful.
"They had two or three penalties for taking jumpers in the air. They were collapsing the maul. They were going around from the wrong side, even once they'd engaged the maul. They were trying to defend our maul but it was being refereed in a very odd way tonight..
"The touch judge thought Bryan Habana carried the ball out - that he caught the ball and then put his foot out. But he was incorrect. They then get the throw in, score a try and Jean de Villiers goes to the ref and says, 'Won't you go have a look at that, you got that wrong?' But it's too late."
The Boks will now shift their attention to Italy, who they tackle in Padova on Saturday (16:30 kick-off).