Australia captain Steve Smith and vice-captain David Warner have stood down from their respective leadership roles for the remainder of the third Test in Cape Town.
Wicketkeeper Tim Paine will act as captain at Newlands, with both Smith and Warner taking the field on Sunday.
Cricket Australia CEO James Sutherland said: "Following discussions with Steve Smith and David Warner they have agreed to stand down as Captain and Vice-Captain respectively for the remainder of this Test match.
"This Test match needs to proceed, and in the interim we will continue to investigate this matter with the urgency that it demands.
"As I said earlier today, Cricket Australia and Australian cricket fans expect certain standards of conduct from cricketers representing our country, and on this occasion these standards have not been met. "
CA chairman David Peever confirmed the board chose Paine, 33, as interim captain.
"The Board of Cricket Australia has endorsed Tim Paine to step in as Acting Captain for the remainder of this Test," Peever said.
"Both Steve and David will take to the field today under Tim's captaincy.
"The Board fully supports the process for an immediate investigation into what occurred in Cape Town. We regard this as a matter of the utmost seriousness and urgency. We will ensure we have all information available to make the right decisions for Australian Cricket."
Smith’s departure from the Test captaincy comes in the wake of revelations the Australians admitted to ball tampering on day three.
Opening batsman Cameron Bancroft was captured using yellow tape to alter the condition of the ball in the afternoon session on Saturday before hiding the foreign object in his pants once the umpires got wind of the wrongdoing.
Smith and Bancroft fronted the media after play and confessed the senior players had devised the plan to manipulate the ball, with Smith taking responsibility for the actions of his team and his rookie opening batsman.
Smith said last night he had not considered standing down as captain, but it appears in the last 12 hours the 28-year-old has had a change of heart.
On Sunday, the Australian Sports Commission called for CA to stand down Smith as captain, a move the governing body was not prepared to do until due process was carried out.
Sutherland confirmed today in Melbourne CA Head of Integrity and Head of Team Performance Pat Howard would fly to South Africa immediately to conduct a review of the incident.
"It's a very sad day for Australian cricket," Sutherland said.
"That can't be the end of it, we have a responsibility to take this further and to understand more about the issue.
"We are extremely disappointed and shocked at what we woke up to this morning, and we are dealing with this issue with the utmost urgency and seriousness.
"We certainly don't have all of the evidence at hand and we need someone to go over there and talk to the relevant people involved to understand what happened and the detail, and then we'll make appropriate decisions as to next steps."
Paine debuted alongside Smith at Lord’s against Pakistan in 2010 and has captained Tasmania 12 times in JLT Sheffield Shield cricket, the last time in November 2014.
The morning after admitting to ball tampering, Smith was noticeably absent as his team warmed up ahead of Sunday's play at Newlands.
Veteran off-spinner Nathan Lyon and Paine were among the first players to arrive at the venue, along with reserve bowlers Chadd Sayers, Jhye Richardson and Jon Holland.
While Paine had a hit out in the nets behind the Kelvin Grove End, Lyon remained close to the centre wicket, eyeing the pitch he hopes will assist him in taking his 300th Test wicket today.
Coach Darren Lehmann and national selector Trevor Hohns were locked in conversation at the Wynberg End as the remaining squad members slowly filtered out to the field.
The customary team huddle held on the field approximately one hour before play was not witnessed on day four, most likely taken place behind closed doors of the away team's dressing room.
The Test squad and coaches emerged from the changerooms and began their warm-ups shortly after 9:30am local in brilliant sunshine, but Smith was not among his players.
The truncated warm-up ended just after 10am, while the South Africans continued their preparation as the look to build on their lead of 294 runs with five second-innings wickets in hand.
Smith said last night senior players had devised the plan at the lunch interval without the knowledge of the coaching staff.
"I'm not naming names but the leadership group talked about it and 'Bangers' (Bancroft) was around at the time, Smith said.
"We spoke about it and thought it was a possible way to get an advantage.
"Obviously it didn't work, the umpires didn't see it change the way the ball was behaving or how it looked or anything like that, so it was a poor choice and deeply regrettable."
He added: "I can promise you this is the first time it's happened and I think I've made it clear, we're regrettable (sic) and we'll move on from this.
"Hopefully we'll learn something from it. I'm embarrassed, I know the boys in the shed are embarrassed as well, and I feel for Cam as well.
"It's not what we want to see in the game, it's not what the Australian cricket team's about, and being the leader of the team I'm incredibly sorry for trying to bring the game into disrepute the way we did today.
"We saw this game as such an important game, not that other games aren't important as well, but an opportunity.
"We've seen the ball reversing quite a lot throughout this series and our ball just didn't look like it was going to go.
"That's a mistake on our behalf again. It's such poor actions and deeply regrettable and certainly won't happen again under my leadership I can promise you."
Bancroft was charged by match referee Andy Pycroft with a Level 2 offence of attempting to alter the condition of the ball. It is understood the Western Australian has accepted the sanction, with the penalty still unknown.
Possible sanctions include a fine of his match fee anywhere between 50 and 100 per cent, with either three or four demerit points added to his record. Four demerit points would trigger an automatic one-Test ban.
Qantas tour of South Africa
South Africa squad: Faf du Plessis (c), Hashim Amla, Temba Bavuma, Theunis de Bruyn, Dean Elgar, Heinrich Klaasen, Quinton de Kock, Keshav Maharaj, Aiden Markram, Morne Morkel, Chris Morris, Wiaan Mulder, Lungi Ngidi, Duanne Olivier, Vernon Philander, Kagiso Rabada, AB de Villiers.
Australia squad: Steve Smith (c), David Warner (vc), Cameron Bancroft, Pat Cummins, Peter Handscomb, Josh Hazlewood, Jon Holland, Usman Khawaja, Nathan Lyon, Mitchell Marsh, Shaun Marsh, Tim Paine, Jhye Richardson, Chadd Sayers, Mitchell Starc.
Warm-up match: Australia beat South Africa A by five wickets. Report, highlights
First Test Australia won by 118 runs. Scorecard
Second Test South Africa won by six wickets. Scorecard
Third Test Newlands, Cape Town, March 22-26. Live coverage
Fourth Test Wanderers, Johannesburg, March 30-April 3. Live coverage