It was the culmination of a chaotic fortnight which began when Mugabe fired his deputy Emmerson Mnangagwa, prompting a military takeover and mass street protests which eventually forced him out, ending a 37-year reign that will best be remembered for its economic ruin.
The resignation letter, which was read out in parliament on November 21, was the result of days of mounting pressure and back-and-forth negotiations with the military generals which were chaired by Mukonori.
"And as soon as he put his signature, (his) face just glowed, really a sign of saying: 'It's done, I have done what I have to do.'
"You could see the handsomeness of the man after signing ... that he has completed his job."
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Close to Mugabe for decades, Mukonori has been involved in mediating nearly all the defining conflicts of Zimbabwean politics, starting in the 1970s when he took part in talks between the guerrillas and colonial ruler Britain that eventually led to independence in 1980.
But most importantly, he too is relieved that the man whom he helped rise to power has finally bowed out.
"It was the best thing he could have done, the man has served 37 years... definitely, it was time to rest," said the softly-spoken priest.
"I was relieved when he signed," Mukonori admitted, recalling the tension as the nation stood on edge following mass street protests and as MPs gathered to impeach him.
Asked if Mugabe's wife Grace was part of the negotiations, he said at times she "would make comments. But we were not negotiating with Grace ... the soldiers were interested in Robert Mugabe."
Following the introduction of Mugabe's controversial land reform policy in 2000 which allowed the seizure of white-owned farms, the farmers turned to Mukonori to intervene.
He also helped the negotiations for the power-sharing government between Mugabe's ZANU-PF and the opposition Movement for Democratic Change, before South Africa's former president Thabo Mbeki and Nigeria's Olusegun Obasanjo stepped in.
During the talks to secure Mugabe's exit, the generals were "very calm", said the 70-year-old priest.
At one point, Mugabe asked to speak to Mnangagwa, who had fled to South Africa after his dismissal in what was the culmination of an increasingly-bitter succession battle between him and the first lady.
So Mukonori rang Mnangagwa and put his cellphone on speaker, allowing them to speak.
"They discussed for a good 10 minutes - really what I call a heart-to-heart talk," he said, recalling how Mugabe begged Mnangagwa to return home, saying: "Come, come here why did you go to South Africa? I was planning to meet you after the dismissal and talk, just the two of us."
Long before the crisis, Mukonori said Mugabe had confided in him that he was going to step down after next year's elections.
While Mukonori is seen as a tough and trusted mediator in Zimbabwe, he is also regarded by some as "controversial" because of his closeness to Mugabe.
That tension was reflected in the preface to a mini biography of Mukonori published in 2006, which says: "There are those who feel that he compromises himself and the church by being too close to the president and his advisers.
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