Mnangagwa received 50.8 per cent of the vote while main opposition challenger Nelson Chamisa received 44.3 per cent.
Police removed opposition officials from the electoral commission stage when they rejected the results. "We thought they were our savior in November but they fooled us", said newspaper vendor Farai Dzengera, saying that the brief dream of an end to decades of repression was over.
"This is a new beginning". Mnangagwa tweeted, after a week that began with peaceful voting Monday but spiraled into deadly violence in the capital Wednesday as the military fired on protesters.
But in the wake of Monday's vote, worldwide observers from both the European Union and the Commonwealth have expressed concern about the election, as has the UN Secretary-General Antonio Guterres.
Speaking after meeting Foreign Affairs and International Trade Minister Dr Sibusiso Moyo at his Munhumutapa offices, Mr Liu said the 2018 elections gave the country a pedestal to rebuild the economy. In a response, the electoral commission said that the "impatient nation" would have to wait longer to learn who will be its next president. Police asked him to step aside.
Later Komichi said the elections were "fraudulent" and "everything has been done illegally".
"We're not part of it", said Komichi, adding that the opposition would be challenging the election in the courts.
Global observers urged the electoral commission to release the tally as soon as possible to avoid more violence after three people were killed on Wednesday in clashes between security forces and opposition supporters.
Opposition supporters protested in Harare over alleged vote-rigging, which led to six deaths on Wednesday.
A lawyer for the Movement for Democratic Change (MDC) Alliance says a search and seizure operation at the party's headquarters in Harare on Thursday afternoon amounts to harassment.
Mr Chamisa, opposition politician Tendai Biti and several others are suspected of the crimes of possession of unsafe weapons and public violence, according to a search warrant.
In Harare, the contrast could not have been starker with November, when hundreds of thousands filled the streets, hugging soldiers and celebrating their role in ousting Mugabe, the only leader Zimbabwe had known since independence in 1980.
It was the first in 40 years not to be dominated by former president Robert Mugabe.
A credible election after past votes were marred by violence against the opposition and alleged irregularities is crucial for the lifting of worldwide sanctions and for the badly needed foreign investment to help Zimbabwe's long-collapsed economy revive.
Instead, observers from the Commonwealth, a group of mainly former British colonies that Mnangagwa had hoped to rejoin, did not mince words in condemning the military's conduct.
Residents in Harare, including Sifas Gavanga, spoke of their frustration at the violence.
The election, the first since the army's removal of 94-year-old Mugabe, passed off relatively smoothly but its aftermath revealed the deep rifts in Zimbabwean society and the instinctive heavy-handedness of the security forces. "I see greater potential for us to expand our corporation", he said.