"This is a tragedy too big to be written," said Astana in a statement, paying tribute to the 37-year-old, who won the Giro d'Italia in 2011.
"Ciao Michele," Astana wrote on Twitter.
The fatal crash happened on a crossroad near his home in central Italy and he leaves behind a wife and two children, Astana said.
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Scarponi was in the twilight of his career but proved his enduring quality on Monday when he took his first victory in four years in the opening stage of the Tour of the Alps.
He outsprinted Briton Geraint Thomas and Thibaut Pinot of France to claim the early lead of the race, a key warm-up event ahead of next month's Giro d'Italia, the first of the year's Grand Tours.
Scarponi was gearing up for another tilt at the Giro, which starts on May 5, when the collision occurred in Filottrano.
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Scarponi won the 2011 Giro after Alberto Contador was stripped of the title for doping. The Italian was himself suspended for doping between 2007 and 2008.
Astana said Scarponi "ended fourth in the Tour of the Alps yesterday afternoon in Trento. Then he went home in Filottrano (Ancona) by car with his masseur and was home in the evening to his family.
"This morning Michele went out on his bike for an early morning training and there the tragedy happened," added Astana.
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