President Cyril Ramaphosa has apologised to Archbishop Emeritus Desmond Tutu for "putting him through a period where he lost confidence" in the leadership of the ANC.
Ramaphosa met with Tutu at his house in Hermanus on Thursday.
"I also want to apologise for that. We put you through a period where you lost confidence in the leadership of the country," Ramaphosa said.
In 2011, Tutu said he would pray together with South Africans for the downfall of the ANC like they did for the fall of the apartheid government. His comments came after the government refused to grant his long-time friend, the Dalai Lama, a visa to attend his birthday celebrations.
At the time a visibly furious Tutu told ANC leaders during a press conference to "watch out", warning them about becoming too complacent after winning every election since 1994.
During that period Jacob Zuma was the president of the ANC and the country. Tutu, who is revered as the moral compass of the country, repeatedly criticised the ANC government for failing to support Tibetans who he said were being "oppressed viciously by the Chinese" despite the international world helping South Africa defeat apartheid.
'This must not be a false dawn'
In a short video, Ramaphosa said: "I am sorry.
"It was not a pleasant moment to hear you as the Archbishop, that we always loved, expressing your loss of hope and loss of confidence.
"I just wanted to say I am sorry we put you through that, but we will work very hard to regain your confidence and make you proud. We will do that," Ramaphosa added.
Tutu, who appeared in good spirits, thanked Ramaphosa for the apology. He also gave Ramaphosa's government his blessing.
"Know that we pray regularly for you and your colleagues that this must not be a false dawn."
Those who attended the meeting said Tutu was overjoyed by the visit and "positive optimism that has engulfed the country" since Ramaphosa replaced Zuma.
"It looks to us that we are on the way to becoming what we were intended to be and we give great thanks to God for you and uphold you and your colleagues and we say Thixo abe nani, anisikelele [God must be with you, and protect you].
"You have to succeed, failure is not an option," Tutu said.