Opposition leader Chakwera has been pronounced the winner with 2.6 million votes, while incumbent president Mutharika has taken 1.75 million and underdog candidate Kuwani over 32,400.
Malawi's opposition leader Lazarus Chakwera has been sworn in Sunday as the southern African country's new president after winning the rerun of a hotly disputed election.
It was a dramatic reversal of fortune for the incumbent Peter Mutharika, whose victory in a May 2019 ballot was overturned by the Constitutional Court over fraud allegations.
Chakwera, a former evangelist preacher, was declared the winner of the election replay held on Tuesday with almost 59 percent of the vote, according to results announced late Saturday.
Malawi is only the second African country south of the Sahara to have presidential poll results overturned in court, after Kenya in 2017.
And it is the first time in the region that a vote rerun has led to the defeat of an incumbent leader.
"I ... do solemnly swear that I will well and truly perform the functions of the high office of the president of the Republic of Malawi and that I will preserve and defend the constitution," the 65-year-old Chakwera said as he took his oath before thousands of supporters.
Opposition candidate Saulos Chilima was sworn in as vice president.
6.8 million voters
Some 6.8 million Malawians returned to the polls on Tuesday after the country's top court found the first election had been marred by widespread irregularities — including the use of correction fluid to tamper with result sheets.
Chakwera was pronounced the winner with 2.6 million votes, while Mutharika took 1.75 million and underdog candidate Peter Dominico Kuwani over 32,400.
Voter turnout was just under 65 percent.
In power since 2014, Mutharika had won 38 percent of the discredited vote last year, just ahead of Chakwera with about 35 percent.
'A government that serves'
"Fellow Malawians, to stand before you is an honour. It's an honour that fills me with unspeakable joy," Chakwera said.
"It is an honour forged in the furnace of your desire and your demand for change."
Addressing supporters in Lilongwe's Freedom Square, Chakwera vowed to restore "faith in the possibility of having a government that serves" and "fights for you."
"There are many of you who did not vote for me in this election and perhaps the prospect of my presidency fills you with fear," he added.
"But ... Malawi is home to you too ... so long as I am its president, you too will prosper."
Chakwera leads Malawi's oldest party, the Malawi Congress Party (MCP), which is the main opposition party and ruled Malawi for three decades from 1964 to 1994 under Hastings Banda's one-party rule.
Mutharika, 79, has not yet commented on his defeat.
On Saturday, he had argued that the election rerun had been flawed, citing violence and intimidation against monitors.
The Malawi Electoral Commission (MEC) dismissed the allegations and said all complaints had been "resolved."
But Mutharika's Democratic Progressive Party (DPP) called on the MEC to annul the results of the second vote and declare a third poll.
Political analysts told AFP they highly doubted the possibility of a second rerun.
Kenya's former prime minister Raila Odinga — who lost to the incumbent in the country's 2017 vote rerun — was among several politicians to congratulate Chakwera.
I congratulate the people of Malawi on the successful and peaceful presidential election and incoming President Lazarus Chakwera on his impressive victory.— Raila Odinga (@RailaOdinga) June 28, 2020
I commend the outgoing President Peter Mutharika for creating the environment for a peaceful and orderly transfer of power.
"I commend the outgoing president Peter Mutharika for creating the environment for a peaceful and orderly transfer of power," Odinga tweeted.
"The election was followed keenly beyond Malawi and is a symbol of hope for those who support democracy in Africa and around the world."
Some celebrations began Thursday night when Malawi’s state broadcaster reported that Chakwera was well ahead with all votes in.
The commission's new chair, judge Chifundo Kachale, while announcing the results acknowledged that “it has been a very interesting journey.”
An attempt by Mutharika’s government to get Malawi’s chief justice to step down just days before the new election had failed amid an outcry. Now the chief justice is expected to swear in Chakwera on Sunday.
Aware that time was running out, Mutharika on Saturday asked the country to “move on peacefully” and respect the presidency.