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.
“When the letter was done, he looked at it, read it through and he just gracefully took his pen and signed,” Mukonori told AFP in an interview in Harare.
“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.”
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.
And negotiating the exit of the man who had ruled one country for nearly four decades was “just another job”.
But most importantly, he too is relieved that the man whom he helped rise to power has finally bowed out.
– ‘I was relieved’ –
“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.”
Mukonori has known Mugabe for more than 40 years and says they are candid with each other. Jesuit-taught, Mugabe has always described himself as a devout Catholic.
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.
– Begged Mnangagwa to return –
During the talks to secure Mugabe’s exit, the generals were “very calm”, said the 70-year-old priest.
And when they presented their 11-point list of grievances, Mugabe did not “wink” because he realised the “seriousness of the issues” and “accepted” them, he said.
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.”
Since Mugabe’s resignation, Mukonori has spoken to him three times, saying he was doing well and had even offered to “support” Mnangagwa.
– A controversial role –
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.
“There are others who appreciate his intervention and believe Fr Mukonori uses his influence for the benefit of the church and the nation.”
Born the village of Mazowe, just north of Harare, Mukonori joined the Jesuit order in 1971 then went on to obtain a masters degree in theology from the University of California at Berkeley.
He is currently the principal and parish priest at Chishawasha mission school, some 40 kilometres (25 miles) outside the capital.
This year, he published his memoirs — “Man in the Middle” — and in 2016, he released a report into the genesis of violence in Zimbabwe.
He was also involved in collecting evidence for a report on the Gukurahundi massacres, a brutal crackdown on opposition supporters that claimed thousands of lives after independence in 1980 which was reportedly directed by Mnangagwa.