He defeated incumbent Peter Mutharika with 58.57% of the vote in Tuesday’s poll, the electoral commission announced late on Saturday.
In February, Malawi’s constitutional court annulled Mr Mutharika’s victory in the May 2019 election, citing vote tampering.
The country was bitterly divided in the run-up to this week’s election.
It is the second African nation to annul a presidential election over irregularities, after Kenya in 2017.
How brave judges rejected a ‘second-rate election’
Following the official result on Saturday, Mr Chakwera said his victory was “a win for democracy and justice,” adding: “My heart is bubbling with joy.”
His supporters took to the streets of the Malawian capital, Lilongwe, sounding car horns and letting off fireworks.
Mr Chakwera is expected to be sworn in on Sunday.
Malawi’s new leader will look to heal the nation
This is a hugely significant moment in Malawi’s political history, and is evidence that neither the courts nor the electorate were prepared to be bullied or influenced by presidential power.
Other countries in Africa have had elections annulled – it happened in Kenya a few years ago – but for the opposition candidate to then go on and win a rerun is unprecedented.
Peter Mutharika’s narrow victory in last year’s poll was cancelled by the Constitutional Court after evidence emerged that correction fluid had been used to alter the vote tallies. He then turned to the Supreme Court for help. Judges there came under a lot of pressure but stood firm. And now the majority of Malawian voters have rejected him.
Mr Mutharika is now crying foul and may mount a legal challenge, but the people of Malawi have chosen Lazarus Chakwera as their next president. The Pentecostal preacher and former theology lecturer will first have to heal a nation that’s been through many months of political turmoil.
Speaking ahead of Saturday’s results, Mr Mutharika said that while he found the election “unacceptable”, it was his “sincere hope that we should take this country forward instead of backwards”.
Why was there a new vote?
A rerun of the 2019 election was ordered after the Constitutional Court found the original ballot had been marred by widespread irregularities.
That election saw President Mutharika narrowly re-elected by fewer than 159,000 votes.
Mr Chakwera, who came second in that election, argued that tallying forms had been added up incorrectly and tampered with.
Uncertainty around the result sparked months of tension, which spilled over into clashes between opposition supporters and police.
February’s annulment led some to celebrate, but Mr Mutharika described it as a “serious subversion of justice” which marked the death of the country’s democracy.
There were concerns over the logistics and safety of carrying out an election in the midst of the worldwide coronavirus pandemic.
Who is Lazarus Chakwera ?
The opposition leader, a former cleric, heads up the opposition Malawi Congress Party (MCP).
Born in Lilongwe to a subsistence farmer, the philosophy and theology graduate has pledged to raise the national minimum wage, among other reforms.