Aru crashed in training in Sierra Nevada, Spain, on April 2, and injured his knee. He called off his plans to race the Giro d'Italia starting May 5 on his home island Sardinia.
He responded to an open letter last week by Nibali, who wrote, "There is a chance to see you at the start of the Giro."
"Vincenzo, I read and I reread your letter," Aru wrote in La Gazzetta dello Sport newspaper today. "And I thought for a long time how good it would be to answer you with a nice one, saying, 'Yes, I will also be at the 100th Giro.' Unfortunately, life often puts the hard evidence in front of us.
"As the intelligent and sensitive guy you've always proven to be, I think you can understand it wouldn't be smart to go to the Giro d'Italia after three weeks without any training. Neither for my team, which has given me confidence, nor for my fans, who were incredibly close in these difficult weeks."
A week after his crash, Aru posted on Twitter a photo of his swollen left knee and said that it prohibits him from starting the Giro in sufficient condition. He damaged the cartilage with the impact.
Watch: Giro d'Italia 2017 essential guide
Aru won the Vuelta a España and placed second and third overall in the Giro. He was one of the favourites with Nibali (Bahrain-Merida), Nairo Quintana (Movistar) and many others including Sky's Mikel Landa and Geraint Thomas.
"The Giro was on my mind and every action and thought was 100 per cent towards this target. Then, as you said, the unthinkable happens and everything seems to vanish like snow in the sun," Aru said.
"With my hand on my heart, I must say that I would like to challenge you on the climbs of the 100th Giro, on Etna and on Blockhaus, up the Stelvio.
"Unfortunately, this injury forced me to stop for more than two weeks by now. And as an example, when I ended my 2016 season, I took three weeks off and started from scratch."
2011 Giro victor Michele Scarponi, who won the opening stage of the Tour of the Alps this week, will lead team Astana now. Aru could race the Tour de France or the Vuelta a España later this year.
"I'll cheer for my team-mates, Michele Scarponi in the first place. But dear Vincenzo, I sincerely hope that too you can do well, maybe allying with 'Scarpa' or with the other strong Italians, there are many, to see the tricolor flag waving higher than the others in Piazza Duomo in Milan."
Thank you for reading 20 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1