General Constantino Chiwenga had challenged President Robert Mugabe over his sacking of the vice-president.
"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", he said in a statement.
Chiwenga noted that there were current purges within the party targeting people who had a history with the liberation struggle while those who did not participate were gaining ground.
Mnangagwa was subsequently fired from the party and has since left the country. However, there is speculation that this could also be a show of force from the military.
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He fled the country and is thought to be in South Africa after issuing a searing five-page condemnation of Grace's ambition and Mugabe's leadership.
The party "reaffirms the primacy of politics over the gun", the statement said.
"Further, we note with concern the attempts by some politicians to drive a wedge between the security services for their own selfish interests".
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.
This comes a day after a statement by army generals urged President Robert Mugabe to cease purges within his ruling party or "the military would be forced to intervene".
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Mnangagwa is now in self-imposed exile.
But the 75-year-old former vice-president has powerful military connections, having served as defence and state security minister.
Analysts said if Mugabe responded to Chiwenga's statement, he would be compelled to choose sides between war veterans and the young turks rallying behind his wife.
Chiwenga said what was happening in the ruling party was a result of machinations of counter revolutionaries who have infiltrated the party to destroy it from within.
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Mnangagwa's removal provides a boost for Grace Mugabe, the wife of the president, who is supported by the largely youthful G40 faction of ZANU-PF to succeed her husband.