Rafik Mohamed, president of the court's constitutional and electoral section, said Assoumani had won with 57.2% of the vote, revising the victor's previous score downwards slightly while greatly boosting a strangely low turnout figure.
"There are grounds to declare him elected in the first round," Mohamed told a press conference.
Opposition leaders rejected the results, describing the vote as fraudulent, but the court dismissed as inadmissible lawsuits seeking its annulment.
"We will not endorse fraud," Aboudou Soefo, a defeated opposition challenger, told AFP. "We will mobilize."
Last week, after the vote, the Comoros capital Moroni was paralyzed by two days of running street battles between stone-throwing youths and armed soldiers.
At least one person was fatally wounded, according to medics.
The opposition had pointed to the unexpectedly low 16% turnout figure in the presidential vote initially announced by the electoral commission as evidence that something was amiss.
The figure was far short of that for governor polls the same day.
According to the electoral commission tally, 189,497 Comorans voted to choose governors for each of the three islands in the archipelago, but only 55,258 cast a vote for president.
'Long and tumultuous'
But on Wednesday the supreme court released new figures saying 191,297 people — 56% of registered voters — had cast their ballot in the presidential race.
It was not immediately clear how the adjustment came about.
"Democracy is in mourning, and the peace and stability of the country is seriously affected," said Daoudou Abdallah Mohamed, a former interior minister and a candidate from the Orange opposition party. "I do not recognize these results."
Last Friday, the U.S. embassy in Moroni expressed concern about the results and urged the electoral commission to "clarify" them.
France, which was the islands' colonial power until independence in 1975, also expressed concern, urging "all Comoran actors to favor restraint and dialogue."
Interior Minister Fakridine Mahamoud described the process as "long and tumultuous." "It's normal there was competition," he said after the final tally was announced.
Assoumani, a 65-year-old former military ruler turned civilian president, has dismissed the concerns.
A former army chief-of-staff, Colonel Assoumani initially came to power in a coup in 1999, before handing over to civilians in 2006.
He returned to politics and won reelection in 2016 in a vote marred by violence and allegations of irregularities.
He has since been accused of creeping authoritarianism. His arch-rival ex-President Ahmed Abdallah Sambi was given a life sentence for high treason for allegedly selling passports.
During this year's campaign, Assoumani hailed his government's construction of roads and hospitals.
But in a country where 45% of the population live below the poverty line, plagued by electricity cuts and water shortages, he has faced popular criticism.