The 2011 winner Scarponi was set to start his 12th Giro d'Italia on 5 May in the Sardinian city of Alghero but was killed by a motorist while training for the event.
Scarponi's death has hit Italian cycling hard and Giro organisers will pay tribute with a dedication of the historic Mortirolo climb in his name and at the finish in Milan on 28 May.
"This climb is well known all over the world and universally respected by cyclists. In 2010, it was the springboard to Michele’s last stage victory at the Giro d'Italia, at Aprica, ahead of Ivan Basso and Vincenzo Nibali," organisers said in a statement.
Scarponi will also be remembered at the start with a minute of silence before flag fall where his Astana team will lead the peloton over the early part of the 206km course to Olbia.
Another initiative will be a doubling of the mountains classification points awarded on Stage 16 from Rovetta to Bormio to the rider who crosses over the Mortirolo in first position.