The Zimbabwe Human Rights NGO Forum says member groups saw soldiers firing "randomly" in downtown Harare and beating up bystanders who were not involved in the protests on Wednesday.
"What they have done is intimidate people in the rural areas saying, "we will kill you if you vote MDC" and so on and then the worldwide observers say this election was free and fair".
The activists are denouncing violent protests but calling the government's reaction illegal and "grossly disproportionate to the violence that it sought to contain".
The two elections observer missions, however, noted that there were complaints that had been logged by opposition parties particularly with regards to the constitution of the ZEC executive, the delay in circulating the voters roll, the layout of the ballot paper as well as alleged abuse of female candidates.
Earlier, MDC leader Nelson Chamisa wrote on Twitter that he had won the "popular vote" in this week's presidential election, in which he faced off against President Emmerson Mnangagwa from the ruling Zanu-PF party.
Police spokesperson Charity Charamba told state broadcaster Zimbabwe Broadcasting Corporation (ZBC) that the three people killed in the clashes had yet to be identified.
Even though the election passed off peacefully, several water cannon trucks patrolled outside the central Harare headquarters of the MDC as its red-shirted supporters danced in the streets. All we know for sure is that one of them is lying.
Masocha said the MDC Alliance supporters presumed victory for their leader based on false impression that Chamisa had countrywide support, when in reality, it was confined to the capital Harare, where it swept out the ruling Zanu-PF party.
In the capital Harare many people went about their usual daily grind, including queuing up for scarce cash outside banks.
The results of the presidential vote has not been released.
The Commonwealth also urged the Zimbabwe Electoral Commission to expedite the announcement of the results of the presidential vote.
ZEC chairperson Priscilla Chigumba said on Tuesday that the final presidential results were due on Saturday.
Pfigu said he was optimistic on election day for the country's first vote without Mugabe, who ruled for almost four decades, on the ballot.
The opposition alleges the elections have irregularities, saying voting results were not posted outside one-fifth of polling stations as required by law.
Zimbabwe's former finance minister claimed that it was a "fact" that he and MDC leader Chamisa, 40, are on a "hit list", without giving evidence of his assertion.
The preliminary findings were released during a media briefing held on Wednesday by worldwide observer missions who have been monitoring the climate leading up to and during the July 30 election.
Mnangagwa had promised a free and fair vote after the military ushered him to power when Mugabe was forced to resign. We've more votes than ED (Emmerson Dambudzo).
For supporters of Zimbabwe's opposition MDC Alliance party, this was a day they had been dreading - the moment their dream of election victory was crushed.
"We are going to have to go to war, go to war against ZANU-PF".