Nibali broke his 10th vertebra on the famous climb up to Alpe d'Huez on July 19 when a fan caught their camera strap on his handlebars.
The Bahrain Merida team says their 33-year-old rider "has undergone a successful surgery" at the La Madonnina clinic in Milan.
The statement on Tuesday adds that the operation "consisted of the injection of biocompatible cement into the body of the vertebra."
Nibali will be released on Wednesday and can return to training on a static bike in a few days.
He will then resume training on the road with an eye on the Vuelta a España, starting 25 August, as well as the World Championships road race on 30 September.
Nibali won the Tour de France in 2014 and the Giro d'Italia twice, in 2013 and 2016. He won the Vuelta in 2010.
