The two teams were at loggerheads over disputed catches on the opening day which South Africa closed 102 runs in arrears with seven wickets intact.
And they also had contrasting views on a referrals system for disputed decisions for this series with England objecting to players making the calls on when to challenge.
The biggest flashpoint came deep into yesterday evening's final session when Hashim Amla was told to remain on the pitch by the South Africans after England captain Michael Vaughan claimed a diving catch at mid-off off the bowling of Andrew Flintoff.
When Amla initially took Vaughan's word, South Africa were effectively 76 for four.
"I have long advocated the use of technology," said South Africa coach Mickey Arthur.
"Funnily enough we wanted the referrals system - because it was going to be trialled in this series - and England were against it.
"I don't think they wanted it trialled in a series that's important but for me if we can get the correct decision at any time that has got to be good for the game.
"That is all we're asking. The referral system takes away the grey area."
England coach Peter Moores explained the home team's position, however, after the International Cricket Council pinpointed this campaign for the increased use of technology.
"People say we didn't want referrals," said Moores. "We support referrals but what we didn't want was players to do the referring.
"We thought the umpires should be taking the responsibility and we made it pretty clear that certain things should be referred and certain things shouldn't. If that was in place we would support it."
Had England claimed that fourth success then they might have held claim to the whip hand heading into this morning's resumption.
But Moores tried to play down the heated atmosphere between the sides when he said: "If your team are shouting to you to stay then you have to stay and wait to see what the umpire says.
"The only thing I would say is that Michael thought he had caught it clean, so obviously claimed the catch.
"But when they were in the huddle there was a big commotion because it was shown on the big screen and it was he who said to the umpires they should refer it.
"He still thinks it was a clean catch."