Myngheer, 22, passed away at 7:08 pm (1808 GMT) in a hospital in d'Ajaccio, on the island's west, surrounded by his family and his partner Emely, Roubaix Metropole Lille said in a statement.
"It is with deep sorrow that we inform you of Daan's death," the team said in a post on its Facebook page. "He lost his last race after fighting like a champion."
His death comes after another Belgian cyclist, 25-year-old Antoine Demoitie, was killed by a motorcycle that ran into him after he fell during the Gent-Wevelgem race on Sunday.
Myngheer, who would have turned 23 on April 13, pulled up in difficulty some 30 kilometres (20 miles) from the line in the first stage of the race at Porto-Vecchio on Saturday.
He suffered a heart attack while in an ambulance, before being transferred by helicopter to hospital where he was put on artificial respiration and fell into a coma.
Myngheer, Belgian junior champion in 2011, turned professional last year with the Verandas Willems team before joining third-division Roubaix Metropole Lille this season.
"Rest in peace champion," the team said.