The Zimbabwe Electoral Commission (ZEC) announced that Mnangagwa, 75, received 2,460,463 votes, representing 50.8 per cent of the total votes, reports Xinhua news agency.
His biggest rival, Nelson Chamisa from opposition MDC Alliance, received 44.3 per cent of the vote.
The other 21 presidential candidates shared the remaining votes.
Mnangagwa said he was “humbled” by his win.
“Though we may have been divided at the polls, we are united in our dreams,” he tweeted.
“This is a new beginning. Let us join hands, in peace, unity and love, and together build a new Zimbabwe for all.”
Mnangagwa is Zimbabwe’s second executive president after Mugabe, 94, who assumed the position in 1987.
The election took place on Monday but opposition supporters protested in Harare over alleged vote-rigging, which led to six deaths on Wednesday, the BBC reported.
The elections were the first since Mugabe was ousted last November. They were intended to set Zimbabwe on a new path following Mugabe’s repressive rule.
It is also the first time in 16 years that the Zimbabwe government allowed European Union, Commonwealth and US election monitors into the country.
More than five million people were registered to vote in Monday’s poll, and there was a turnout of 70 per cent.