Bonyongwe, who until now has operated under the radar as Mugabe's chief spy, was on Monday appointed as the country's new Justice minister - replacing Vice President Emmerson Mnangagwa - who has been performing the dual roles of VP and Justice guru since December 2015.
The former CIO boss holds a law degree from the University of Zimbabwe, where he also won a Book Prize as the co-best student in his stream.
During his swearing-in ceremony on Tuesday, Bonyongwe said he was relishing the opportunity of serving in his new post.
"It is my hope that I will be able to make some positive contributions to my country. That is something that has always motivated me. I view it as a deployment by my leadership and therefore, I look at it from that context and I will go there and do my best," he said.
But with the 2018 elections looming large - amid growing infighting and divisions in the ruling Zanu-PF - analysts said yesterday that Mugabe's choice of Bonyongwe to head the ministry was telling.
"He is an able legal mind and the hope will be that he will put it to good and productive use during his tenure.
"A former soldier and spy chief in charge of justice seems ominous, not just for Mugabe's internal rivals, but also for the broader opposition movement. It (Justice ministry) is the political authority in charge of elections and will therefore have a huge influence upon Zec (Zimbabwe Electoral Commission)," said constitutional law expert Alex Magaisa on his blog.
"It represents yet another influential hand of the security structure in elections. And who knows, he could be a dark horse in the (Zanu-PF) succession race and his transfer to the political arena should be carefully watched.
"Of the current generals, he is the one who boasted a more superior intellect although he was less known and is more discreet by virtue of his role in the spy agency," he added.
Political analyst McDonald Lewanika said Bonyongwe's appointment to the Justice ministry was not just unexpected, but could also be viewed from many other perspectives.
"Although a qualified and purported brilliant legal mind, his appointment ahead of elections suggests a takeover of the legal and electoral apparatus by the intelligence community.
"Speculation has been rife in the past that the CIO has deployed its members to occupy key positions in the Zec secretariat, and thus Bonyongwe's ascension could ensure effective and close control of this critical body ahead of elections," Lewanika told the Daily News.
"Although Bonyongwe is a retired general, this move also appears to be aimed at checking not just the Lacoste faction, but also the current military establishment which has been unequivocal in its support of the man that Bonyongwe replaces, VP Mnangagwa, whom Bonyongwe has never appeared to prefer as a principal.
Mugabe has previously hinted at his plan to retire security chiefs whom he has openly accused of meddling in Zanu-PF's internal power wrangles.
In July, he told Zanu-PF supporters in his home province of Mashonaland West in Chinhoyi that "politics led the gun", suggesting that the military and other security organs were positioning their preferred candidate to succeed him - warning in the process that he could be forced to retire some security commanders.
While the security establishment is deeply loyal to Mugabe, whom they see as a steadying hand in power - amid intense jockeying over his succession at both State and party level - top commanders have also been said to be backing Mnangagwa to succeed the nonagenarian.
At the recent Chinhoyi youth interface rally, the 93-year-old also appeared to give his biggest hint yet that he planned to neutralise security chiefs by awarding them top government posts.
"We give immense respect to our defence forces. Most of those in leadership are persons we were with outside the country and we continue to respect them as revolutionaries.
"Yes, they will retire and we must find room for them in government so they don't languish . . . so they continue the struggle now . . . political struggle together with all of us in the leadership of the country, and this is what we expect to happen," Mugabe said then.
Piers Pigou, a senior consultant with the International Crisis Group, said Bonyongwe's appointment appeared to be Mugabe's plan to contain Mnangagwa - more than promoting government efficiency.
"Bonyongwe is now in charge of Justice and of government business in Parliament - areas where he is something of a novice and will require significant guidance.
"And of course, we can see this is also part of the general push-back and containment of VP Mnangagwa.
"Taken together, this seems to be more about internal power politics within the ruling party than the promotion of good and efficient governance," Pigou said.
Zanu-PF is deeply-divided over Mugabe's succession.
A faction of young Turks going by the moniker Generation 40 (G40), which has been locked in a vicious battle with Mnangagwa's backers, Team Lacoste, has renewed its resolve to finish off the Midlands godfather who on Monday lost significant control of key institutions when Mugabe demoted and fired ministers perceived to be loyal to him.
Relations have worsened between G40 and Team Lacoste since Mnangagwa was airlifted to South Africa after falling sick at a Zanu-PF rally in Gwanda two months ago, amid claims that he had been poisoned by his rivals in the brawling party.
Meanwhile, Mugabe has consistently batted away calls to name a successor - insisting that it is against the Zanu-PF constitution which demands its members to call for an extra-ordinary congress to choose a new leader if circumstances call for such a move.
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