Australian cricket captain Steve Smith is "incredibly sorry for bringing the game into disrepute" but says he won't resign as skipper after a ball tampering controversy erupted in South Africa overnight.

Australian batsman Cameron Bancroft was summoned for a chat to the umpires after they spotted something suspicious in his pocket before the tea break of day three in the Test match being played between the two countries.

He was caught fiddling with a small yellow object in his hand but was waved away after showing a sunglasses case to the umpire. Footage later confirmed Bancroft slyly put a yellow object into his underpants before facing the umpires.

Veteran commentator Mike Haysman and former South African skipper Graeme Smith both put the sword to Aussie captain Steve Smith, claiming Bancroft and the touring team faced "severe" repercussions.

Smith and Bancroft fronted up to the media after the match, with the latter confessing the object used to alter the ball was yellow tape.

"I was in the wrong place at the wrong time," Bancroft said. "I was nervous about it. There are hundreds of cameras around."

When asked who was responsible, Smith said it was a decision made by the players and not the coaching staff.

"It was purely the players, and the leadership group (that were responsible)," Smith said.

"We saw this game as such an important game. We've seen the ball reversing ... so that's a big mistake on our part.

"I'm incredibly sorry for bringing the game into disrepute ... The boys in the shed are embarrassed. I feel for Cam as well. I am embarrassed to be sitting here."

Smith said he wouldn't be stepping down from the captaincy role, claiming he felt he was still the "right person" for the role, but accepted responsibility for the ugly incident.

The day's play wrapped up with South Africa stamping its foot down on Australia as the Proteas built a strong lead of 294.

The Aussies took five wickets throughout the day but weren't able to instigate any breakthroughs before veteran AB de Villiers and Quinton de Kock saw the day out comfortably as an early stumps was called due to bad light.

An impressive 84 from rising opener Aiden Markram was the highlight for the home side.

Former Aussie leg-spinner Shane Warne was heavily critical of the footage of Bancroft's "undies-gate" controversy.

"I don't care who you are, you can't tamper with the ball," Warne said during the tea break.

"I don't care if it's Australia or South Africa. You can't do (that). It looked like what we all think it was. To me that'd be really disappointing. A lot of the Australian sides I've played in, there was never anything like that."

"I don't think he's taken it upon himself to put it in his pocket," he said. "Now, who has told him to do that? It's important to find out that. You've got to own up."

"In my opinion, he's tampered with the ball," Graeme Smith said after tea. "It's quite obvious. I really am amazed, with the footage, that the umpires have done nothing about it.

"If it is correct, there's some tough questions you've got to ask of Steve Smith and Darren Lehmann. They're the leaders and (Bancroft) is the one who has played seven or eight Test matches. It's obviously a decision taken behind the scenes."

CRISIS MEETINGS? SMITH LEAVES THE FIELD

Steve Smith conspicuously left the field in the final session of play after the ball tampering controversy erupted, leaving David Warner to briefly skipper the side for the evening.

Fans speculated the Aussie captain was in a crisis meeting with coach Darren Lehmann in anticipation for the storm after the day's play.

Umpires were repeatedly scolded for their inaction upon the revelation Bancroft had hidden an object in his underpants.

AUSSIES SLAMMED FOR HYPOCRISY

South African legend Mark Boucher led the chorus of critics in accusing Australia of double standards after coach Darren Lehmann blasted home crowds on the tour for their "disgraceful" personal abuse towards his players and their families.

Lehmann made the comments after a spectator taunted David Warner when the opener was making his way up the race after being dismissed on day two, causing the left-hander to stop and turn back to the man before security intervened.

Speaking after play, Lehmann said Cricket Australia had written to Cricket South Africa about the hateful insults being hurled towards the visiting camp.

"It's been disgraceful. You're talking about abuse of various players and their families and personal abuse," Lehmann said. "It shouldn't happen.

"Banter, that's fine. Banter is good-natured fun by crowds but they've gone too far here ... it's been poor.

"As soon as they cross the line and they talk about players' families the whole time and getting abused like that, it's just not on."

Boucher took to Twitter to accuse the Aussies of being hypocritical — saying Australian crowds were guilty of "ridiculous" racism."

Boucher also retweeted another social media user who mocked Lehmann's double standards, referencing his remarks ahead of the 2013/14 Ashes when he encouraged Australian crowds to abuse English quick Stuart Broad for "blatant cheating".

Lehmann was referring to Broad refusing to walk and being given not out after he edged a ball to slip during the 2013 Ashes in England.

Boucher's former South African teammate Paul Harris was on the wicketkeeper's side, saying Australian crowds were just as bad.

Former South African captain Graeme Smith, who is doing television commentary for this series, backed up Boucher too.