Scarponi was training near his home of Filottrano, near Ancona, when he was hit by a van at a crossroad, Team Astana said.
According to Italian media reports, the Astana cyclist died on the spot and was unable to be revived by emergency services which arrived promptly.
Team Astana called it “a tragedy too big to be written” in a statement.
“We left a great champion and a special guy, always smiling in every situation, he was a real mile stone and a landmark for everyone in the Astana Pro Team,” it added.
Scarponi is survived by a wife and twin sons. He had returned home after finishing fourth in the Tour of the Alps on Friday in Trento. He won the first stage on Monday.
Scarponi had posted a photo on Twitter on Friday night, with his sons on his back and the caption: “Even if only for a day I thought I’d bring home two leaders’ jerseys.”
Scarponi was awarded the 2011 Giro trophy after Alberto Contador was stripped of the title because of doping.
The Italian had also faced doping sanctions. He was banned for 18 months in July 2007 following the long-running Operation Puerto doping scandal, while he served a three-month suspension from the end of 2012 after working with the banned physician Michele Ferrari.
Scarponi had been named as Astana’s leader for the Giro d’Italia, which starts in less than two weeks, after Fabio Aru pulled out with a knee injury. “An infinite tragedy. Words don’t exist. Rest in peace my friend,” Aru tweeted.
Former team-mate Vincenzo Nibali wrote: “I don’t know, I can’t cope! I don’t have words my friend...”
Scarponi was known for his sense of humour – he often started training rides with his parrot on his shoulder, posting videos which quickly went viral.