The army meanwhile said on state television that it was not a coup.
Several cabinet ministers and other leaders have allegedly been arrested.
Magaisa, the former political aide, said the treatment of those being detained will be telling of what comes next.
There were reports of multiple explosions in the city and a heavy presence of armed soldiers in the early hours of Wednesday morning local time.
A power struggle between Zanu-PF factions – independence era veterans and the “G40” group – is thought to have destabilized the party.
Martin Rupiya, an expert on Zimbabwe military affairs, said the army appeared to be moving to put the squeeze on Mr Mugabe.
This unprecedented intervention by the military has drawn angry responses from supporters of Mugabe, according to the Zimbabwe Mail which describes the country as “on the brink”.
Mnangagwa’s dismissal left Mugabe’s wife Grace, 52, in prime position to succeed her husband as the next president – a succession strongly opposed by senior ranks in the military.
Senior Zimbabwe government officials who wanted to remain anonymous told eTN this morning the situation in Harare was tense and unsafe.
Many had expected Grace Mugabe to be appointed vice president in Mnangagwa’s place at the Zanu-PF special congress next month.
The announcement capped days of political surprises that started with the firing of Vice President Emmerson Mnangagwa last week, followed by a statement from the head of the armed forces, who warned Monday that the military will intervene if the purge continued.
“To both our people and the world beyond our borders, we wish to make this abundantly clear this is not a military takeover of government”, Maj.
In the statement, the ruling party said it stood by the “primacy of politics over the gun” and accused General Chiwenga of “treasonable conduct … meant to incite insurrection”. It’s looking increasingly likely Robert Mugabe will indeed be ousted from power in the near future, and he’s getting Grace Mugabe out of Zimbabwe.
Mugabe was elected Prime Minister the following year when his ZANU-PF secured 63 per cent of the national vote. He said this earlier in the day.
Mr Mnangagwa is one such veteran of the 1970s war which led to independence.
He warned that the military was ready to deal with any acts of dissent. Areport said they would face charges of undermining the authority of the President, by singing “We hate what you’re doing” as the first lady spoke.
“Life is going on”.
“From the direction of his house, we heard about 30 or 40 shots fired over three or four minutes soon after 2:00 a.m.”, AFP quoted witnesses close to Mugabe’s compound as saying.
“The government’s silence on the military deployments seem to confirm that President Mugabe has lost control of the situation”, Robert Besseling, of the London-based EXX Africa risk consultancy, said. But he managed to get the backing of the opposition and the army.