He is the second Belgian cyclist to die in as many days after Antoine Demoitie was struck by a motorbike during Belgium's Gent-Wevelgem race.
Myngheer, who turned professional last year, had been in an induced coma.
His team, Roubaix Metropole Lille, said in a statement: "He lost his last race after fighting like a champion."
Myngheer pulled up in difficulty 20 miles from the line in the first stage of the race at Porto-Vecchio on Saturday.