Mnangagwa, of the ruling ZANU-PF party, won 50.8 percent of the votes cast, with his closest rival Nelson Chamisa, of the Movement for Democratic Change (MDC) Alliance, garnering 44.3 percent, Zimbabwe's electoral commission announced in the capital, Harare, early on Friday.
A candidate needed more than 50 percent of the votes to secure an outright victory in Monday's poll.
Mnangagwa, a former vice president popularly known as "the crocodile" because of his political shrewdness, has been in power since November 2017 following the resignation of long-time President Robert Mugabe in the wake of a military intervention.
Shortly after the announcement of the results, Mnangagwa took to Twitter to thank Zimbabweans and hailed "a new beginning".
The 75-year-old has vowed to bring in foreign investment and create much-needed jobs.
Paul Mangwana, spokesperson for ZANU-PF, said the ruling party was "very happy with the results".
"We're very pleased that our president has won because it means that we can now deliver the change that's promised to the people," he told Al Jazeera.
He added that if the opposition had "the courage to claim fraud, then they must have the courage to face us in court - we are ready for the battle and we will defeat [them] the same way we defeated them at the polls."
Opposition candidate Chamisa on Friday said the release of "unverified fake" results was "regrettable". "The level of opaqueness, truth deficiency, moral decay & values deficit is baffling," he tweeted.
Earlier Morgan Komichi, MDC Alliance chairperson, described the results as "bogus".
"We were not given time to verify the results. This result that you are hearing has not been verified. These are bogus figures. They are bogus results, and we believe that a lot of the figures have been inflated," he said, speaking outside the National Results Centre.
ZANU-PF, which has ruled the southern African country since independence in 1980, also won a clear majority in the 210-seat parliament.
The ruling party won 145 seats, followed by the MDC which took 63. The National Patriotic Front and an independent candidate also picked up one seat each.
The streets of Harare remained deserted on Thursday, with shops closed a day after clashes between security forces and MDC supporters, who claimed foul play in the vote counting of the parliamentary poll.
At least six protesters were killed and 14 wounded.
Witnesses told Al Jazeera on Wednesday that soldiers used live rounds to disperse the demonstrators. Security forces also used tear gas and water cannon at them.
Even before the presidential poll results were released, the MDC accused the government of rigging the election - the first without Mugabe in the ballot in decades.
"We have won this election and Mr. Mnangagwa knows it - our supporters must be calm and anticipate massive celebrations," Chamisa told reporters earlier on Thursday, after visiting wounded protesters at Harare's Parirenyatwa hospital.
EU observers: Un-level playing field
More than five million people registered to vote, while a total of 23 presidential hopefuls run for the country's top seat - all first time contenders.
It is the first time since the end of white-minority rule that such a large number of candidates competed for the Zimbabwe's presidency.
The Electoral Commission said on Wednesday 1.3 percent of registered voters could not cast their vote because they presented the wrong documents at polling stations.
Observers from the European Union criticised the poll, saying there was "un-level playing field" and "intimidation of voters".
"These elections were seen as a critical test of Zimbabwe's reform process," Elmar Brok, the EU mission's chief observer, said on Wednesday.
"In some senses, up to this point, the conduct of the polls has had a number of positive features, but in other senses, serious concerns remain," added Brok.