Mr Zuma spoke to the 93-year-old leader who said he was "confined to his home" but "fine", according to an official statement released by the South African president's office.
He is also in contact with the Zimbabwean Defence Force (ZDF), the statement said.
South Africa said it was sending envoys to meet with Mr Mugabe and the military.
The statement from the South African President came after AFP reported gunfire near Mr Mugabe's private residence in Harare in the early hours of the morning.
"From the direction of his house, we heard about 30 or 40 shots fired over three or four minutes soon after 2.00 am," a resident who lives near the leader's mansion in the suburb of Borrowdale said.
After the army took control of state TV early on Wednesday, a spokesman announced it was targeting people close to Mr Mugabe who it said caused "social and economic suffering".
A statement read out by Major General Moyo gave assurances the 93-year-old leader and his family were “safe and sound”. The leader has not yet appeared or given a statement himself.
The army has denied staging a military coup, saying that once it has completed its “mission”, the country will return to “normalcy”.
Mr Mugabe has been in power since Zimbabwe's independence from white minority rule in 1980.
The military takeover comes after the leader last week fired vice president Emmerson Mnangagwa.
Mr Mnangagwa – who enjoyed the military's backing – fled Zimbabwe last week but said he would return to lead the country.
More than 100 senior officials allegedly supporting him have been listed for disciplinary measures by a faction associated with Mr Mugabe's wife Grace.
The first lady appeared positioned to replace Mr Mnangagwa as one of the country's two vice presidents at a special conference of the ruling party in December, leading many in Zimbabwe to suspect she could succeed her husband.
Ms Mugabe is deeply unpopular with some Zimbabweans because she is seen to spend lavishly spending as many struggle.
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