The judiciary cancelled President Peter Mutharika's narrow win in February over "systematic and grave" irregularities. Mutharika, who has been in power since 2014, called the ruling a "coup".
Malawians are voting on Tuesday in a re-run of a discredited presidential election seen as a test of Africa's ability to tackle ballot fraud, but the country's president has said reports of violence called the integrity of the contest into question.
Incumbent President Peter Mutharika, 79, is looking for a second and final five-year term in office and is running against Lazarus Chakwera, 65, leader of the main opposition Malawi Congress Party.
The Constitutional Court on February 3 struck down Mutharika's victory in the May, 2019 election, citing evidence of voting fraud, including thousands of ballots that appeared to have been altered using typing correction fluid.
His disputed win also sparked months of anti-government protests, a rare sight in Malawi. Last week hundreds of lawyers also protested when Mutharika tried to retire Chief Justice Andrew Nyirenda, forcing the president to back down.
President calls electoral foul
After voting at a school in the tea farming district of Thyolo, southern Malawi, Mutharika decried what he described as violence in opposition strongholds in central Malawi.
"It is very sad. Our secretary general has been beaten up," he said. "Those causing the violence are desperate. How then will the election be credible?"
There was no independent confirmation of the alleged unrest, although the electoral commission said it had received reports of violence.
After voting in the capital, Lilongwe, Chakwera told his supporters, "There is no reason really to resort to violence ... The vote itself is the fight we need."
He added that he believed the election would be fair this time.
The judiciary's ruling echoed one by a Kenyan court in 2017, which cancelled President Uhuru Kenyatta's election win. Both were remarkable on a continent in which judges often serve as a rubber stamp to executive power.
The vote looks too close to call. Malawi has since ditched its "first-past-the-post" system so the winner has to get more than 50 percent.
'I pray my vote will count'
About half of Malawi's predominantly farming population live in poverty. Lying on a lake at the southern tip of the Great Rift Valley, Malawi mostly exports tobacco and tea.
In the May 2019 poll, Mutharika got 38.57 percent, 3 percentage points more than opposition leader Lazarus Chakwera, and less than 10 points ahead of a third candidate, Deputy President Saulos Chilima.
The 47-year-old Chilima has now backed Chakwera, 64, which would give them a majority if they can combine their previous votes.
Mutharika's Democratic Progressive Party is in an alliance with the southern African nation's ex-ruling party, the United Democratic Front, which got less than 5 percent last time.
"I'm glad to vote again. This I pray, that my vote will count," said Bernado Simbi, 36, a domestic security guard after voting for Mutharika in a school near Chileka Airport, north of the commercial capital Blantyre.
Mutharika, a former law professor, has revamped Malawi's roads and boosted electricity while also taming inflation. Yet critics accuse him of doing little to tackle corruption.
"The government has lost the anti-corruption fight (and) the opposition has taken advantage," said Happy Kayuni, political science lecturer at Malawi University.
Chakwera has made graft a central pillar of his campaigns.
Covid-19 restrictions will make it tricky for foreign observers, who did not detect fraud last time.