Troops backed by armoured vehicles opened fire on Wednesday to clear the capital's streets of demonstrators who accused Mnangagwa's ruling party of trying to rig Monday's presidential election.
"You said you were better than Mugabe you are the picture of Mugabe", shouted one young male protester wearing a white T-shirt. "We know that people will be beaten - especially in rural areas, like what they were doing before", said Harare shop worker Tracy Kubara, 26.
The man died after being shot in the stomach, an AFP photographer said, confirming that he died at the scene.
Zimbabwe's ruling ZANU-PF party won the most seats in parliament, official results showed Wednesday, as the count continued in the presidential race and the opposition MDC cried foul, alleging widespread fraud.
Thousands of supporters of the opposition Movement for Democratic Change chanted anti-government slogans in Harare and faced off against a heavy police presence, fearing that their candidate, Nelson Chamisa, would have the election stolen from him.
Police confirmed the death toll of three, and Mnangagwa issued a statement blaming the opposition for the unrest and fatalities.
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Border Patrol, defended the administration's intentions, saying, "We do not leave our humanity behind when we report for duty". Citizenship and Immigration Services, which oversees legal immigration and guest-worker visa programs.
Nkululeko Sibanda, MDC alliance spokesman, said: "The results are a gimmick to try and prepare Zimbabwe for a rigged election".
"Let me also warn such individuals and groups that no-one is above the law", home affairs minister Obert Mpofu said.
It is a lesson for the opposition that in future they should not lose sight of the bigger prize.
Police patrol outside the Zimbabwe Electoral Commission offices in Harare, Zimbabwe.
The riots surged up to the fence of the Rainbow Towers Hotel & and Conference Centre, where the electoral commission has been announcing results and many worldwide election observers are staying.
The European Union said the elections were competitive and freedoms were respected, but that there was a lack of a "truly level playing field". It called for transparency in the release of results.
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The deployment of soldiers and their beating of unarmed protesters tarnished incumbent President Emmerson Mnangagwa's attempts to rid Zimbabwe's derelict status after decades of repression under his predecessor, Robert Mugabe.
But the mission welcomed an "improved political climate" and largely peaceful election, a break from past violence under longtime autocratic leader Robert Mugabe.
The Zimbabwe Electoral Commission (Zec) has announced 122 seats for Zanu-PF so far, and 53 for MDC Alliance, ZBC state media reported.
His bombshell claim came on Tuesday just hours before the first official results showing Zanu-PF had won a thumping majority in the Zimbabwe election emerged.
Alternatively, many Zimbabweans wonder whether the ruling establishment, including the military, would accept a win for the main opposition leader, Nelson Chamisa. We have won the popular vote.
As results have yet to be officially announced by the ZEC sources counting the ballots have said it is "close".
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Meanwhile the parties defeated in the July 25 elections said they would ally against the "stolen mandate" of Mr Khan. Imran Khan is trying to form a coalition government that would put his Pakistan Tehreek-e-Insaf party in charge.
Commission chairwoman Priscilla Chigumba, a high court judge, has flatly denied allegations of bias and strongly disputed accusations of rigging.