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.
After marathon six-month hearings broadcast on public radio, the court on Monday declared that Mutharika was "not duly elected."
Mutharika, who will remain president until the fresh polls, has the right to appeal the verdict, which is expected to stoke turmoil in the normally peaceful southern African country.
Amid heightened tensions, both Malawi officials and the international community are urging people across the country to uphold the rule of law and remain calm.
The 78-year-old Peter Mutharika was sworn in for a second five-year term as Malawi’s president under the shadow of vote rigging.
Malawi's President Peter Mutharika wins the elections with 38.57 percent of votes narrowly securing another five-year term, the country's electoral commission says.
Electoral commission says President Peter Mutharika, who is fighting for a second five-year term in office, has 40.49 percent of the vote.
Polls closed at 6:00 pm (1600 GMT) after a closely-fought election between the incumbent President Peter Mutharika and his two rivals in a race that focused on corruption allegations and economic development.
Malawi's President Arthur Peter Mutharika declared a state of disaster in the region late on Friday, after a storm caused rivers to break their banks, leaving villages underwater, and in some areas knocked out power and water supplies.
Malawi police has so far arrested 140 people in clampdown after ‘vampirism’ killings. Nine people have died since the beginning of the last month.
Malawian President Peter Mutharika says Malawi in state of national disaster as drought worsens living conditions
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