"I have never stopped telling him God called him to be a pastor, a preacher, a comforter of the afflicted and afflicter of the comfortable," Tutu said in a statement.
"I have nagged him since the 1990s to heed the call of God not as a politician but as a pastor with outstanding intellectual and oratorical gifts, one who is blessed with a sharp creative intellect.
"I cannot say how thrilled I am that Allan has followed this path and agreed to serve the people through God, rather than through political parties," said Tutu.
Boesak quit the Congress of the People today, saying its structures were in disarray.
"From the very beginning the party structures, such as they were, were characterised by faction fighting, strife, pitched battles for political supremacy and duplicity... At this point the party structures continue to be in disarray."
Boesak "expressly" said he did not want a leadership position in Cope when he joined it in December 2008. "It was only after the severest pressures that I conceded to assist the party in the elections."
Deep resentment was caused within the party "by the irregularities with the list process and the interim leadership situation persisted and made normal work almost impossible", Boesak said in a statement.
This is an apparent reference to reports of in-fighting between Mvume Dandala - elected as Cope's presidential candidate - and party leader Terror Lekota.
Boesak said many "good, hard workers" in the party had been suspended because they dared to criticise the leadership. "It seems that the mud is rising. I have no desire to subject my family, myself or my calling to serve our people to these sorts of indignities and destructive politicking."
Cope spokesman Phillip Dexter brushed aside Boesak's criticism, saying it was never going to be easy to launch a new political party. "We've received his resignation with regret. He joined the party when we launched... so obviously people had high hopes for his involvement. The kind of challenges he pointed out... are ordinary challenges when you are dealing with a new organisation. We wish him the best in his future endeavours," Dexter said.
Cope also issued a statement on Tuesday, saying it was celebrating the first anniversary of its national convention held in Sandton, Johannesburg last year in November.
"Those who predicted Cope's demise have been proved wrong. The CWC [central working committee] was satisfied that the party is growing from strength to strength," it said.
Boesak's resignation is not the first to hit the party that saw the light late last year under the leadership of ex-African National Congress veterans Lekota, Mluleki George and Mbhazima Shilowa.
The trio were all vocal supporters of ex-president Thabo Mbeki, who was ousted by the ruling party's national executive committee.
Two senior Cope leaders, Simon Grindrod and Lynda Odendaal, resigned in recent months, expressing disappointment with the way the party was being managed.
Cope is the third-biggest party in Parliament and has been increasingly working with the official opposition, the Democratic Alliance.
Boesak said "working for the integrity of this democracy of the people of South Africa is what I have always been called to do", adding that he would return to work for the "globalisation project" with churches in South Africa and Germany.
"Here, as before, I can work with dignity and purpose."
In the meantime, he would continue to pray for Cope. "My prayer is that Cope will find that hope and vision again and so fulfil the promise it had made to the people of South Africa now almost one year ago."
Tutu said Boesak had now joined "God's party".
"Some may say that Allan, as a member of the human race, is not perfect. But few would argue that he is not perfectly equipped to inspire a new generation of active and involved citizens - as he did once before. Welcome back to God's party," said Tutu.
Boesak, who was convicted of fraud in 1999 but later pardoned, recently released his autobiography, "Running with Horses: Reflections of an Accidental Politician", in which he maintains his innocence.
The fraud and theft conviction related to more than R1.5 million of foreign donor funds in the apartheid era.
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