General Constantino Chiwenga, who appeared at a news conference with another 90 senior army officers, did not refer to anyone by name but is believed to be referring to President Mugabe.
Already they have reacted angrily to Mnangagwa's sacking and in retaliation; they purportedly fired President Robert Mugabe and his wife First Lady Grace from Zanu PF.
Zimbabwe's army chief on Monday demanded an end to the purge in the ruling Zanu-PF party, and warned the military could intervene.
"We must remind those behind the current treacherous shenanigans that, when it comes to matters of protecting our revolution, the military will not hesitate to step in", Chiwenga said in a statement read to reporters at the news conference.
The expulsion of Mnanggwe, a former minister of defence and state security, had removed a potential successor to Mugabe, the 93-year-old president and leader of the ruling ZANU-PF party.
The speech came a day after Mugabe publicly criticised Mnangagwa for the first time during a speech at a rally on November 4.
Mnangagwa - whose nickname is the "Crocodile" - defiantly told Mugabe that the party was "not personal property for you and your wife to do as you please".
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Mugabe's 37 years in power has been anchored by support from the military, which has always said it will not back anyone for president who did not fight in the liberation war.
Mr Mnangagwa previously served as defence and state security minister.
The choice of KGIV was also poignant for an unprecedented statement that can only be rivalled by late General Vitalis Zvinavashe's infamous "straight jacket' statement issued on the eve of the 2002 presidential election and credited with tipping the scales in Mugabe's favour against a popular opposition leader Morgan Tsvangirai".
The purging in the party had plunged the country into a crisis, he said.
"There is distress, trepidation and despondence within the nation", he continued.
"As a result of the squabbling, there has been no meaningful development in the country for the past five years".
Chiwenga said ZANU-PF had since 2015 been rocked by infighting, which had afflicted the economy, causing serious cash shortages and soaring prices of basic commodities - rare criticism of those in government by the military.