Grace has publicly called on her husband to name a successor, ratcheting up tensions with Mnangagwa, a regime loyalist who has been widely tipped to succeed Mugabe.
But the open warfare between Grace and Mnangagwa has apparently left Mugabe furious.
Mugabe has repeatedly condemned factionalism within the party in thinly veiled rebukes to Mnangagwa and his wife's public posturing.
Mnangagwa's replacement as justice minister, Bonyongwe, is a retired army major general, who was the director general of the country's feared intelligence service.
Finance minister Patrick Chinamasa, who has been tasked with reviving the country's ailing economy, was replaced by Ignatius Chombo, who was home affairs minister.
Mnangagwa is one of the two ministers who were pushed out, while a total of ten others reshuffled, in a first shake-up since 2015.
Zimbabwe goes to the polls in 2018, and his party has endorsed him as its presidential candidate to face a coalition of opposition parties.