Thousands of people were at the 60,000-seat stadium in Harare to watch the swearing-in ceremony following a dramatic few days in Zimbabwe.
After returning from exile in South Africa, Mnangagwa told cheering crowds earlier this week: “I pledge myself to be your servant. I appeal to all genuine patriotic Zimbabweans to come together.
“We work together. No-one is more important than the other – we are all Zimbabweans.”
Zimbabwe’s main opposition said it wanted incoming president Mnangagwa to dismantle all pillars of repression that helped sustain Mugabe’s 37 years in power.
In its first official comments since Mugabe resigned on Tuesday, the MDC said it was cautiously optimistic that a Mnangagwa presidency would not “mimic and replicate the evil, corrupt, decadent and incompetent Mugabe regime.”
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Mnangagwa and his wife Auxilia entered the National Sports Stadium to a rendition of the national anthem before Bishop Mutendi led the stadium in prayer.
He took his oath of office which was followed by before a flypast and a gun salute. The new president will address the nation shortly.
Mr Mugabe did not attend the ceremony, making this a particularly unusual presidential transition.
Millions of people across the country have been celebrating the end of Mugabe’s presidency, which has breathed new hope into a country that has spent years suffering under his long and brutal leadership.
His 37-year presidency was brought to an abrupt end by a battle to succeed him, which pitted vice president Mnangagwa against Mugabe’s 52-year-old wife Grace.
Mnangagwa, popular with the military and dubbed ‘The Crocodile’ because of his reputation for stealth and ruthlessness, has spent several days in South Africa after he was ousted by Mugabe last week in the clearest move yet that he was paving the way for his wife Grace to succeed him.
Grace Mugabe, nicknamed ‘Gucci Grace’ for her love of expensive fashion, was widely despised and many Zimbabweans feared she would have continued Mugabe’s brutal reign.