Borgonovo, who wrote his own autobiography despite only being able to make use of his eyes to control a computer to write it, had been suffering from the disease since 2006. He leaves a wife and four children.
He made his illness public in 2008 when he also launched the Stefano Borgonovo foundation.
ALS is the most common form of motor neurone disease and also claimed the life of ex-Genoa captain Gianluca Signorini at the age of 42 in 2002.
Known as Lou Gehrig's disease in the United States after the baseball great it killed in 1941, ALS attacks the motor neurons of the brain and spinal cord, causing swift muscle degeneration.
In the general population there are around 2.5 cases per 100,000 people a year. Statistics have that there are far more cases of ALS among ex-professional footballers in Italy than among the general public.
Borgonovo started his career with Como and played for Milan from 1986 to 1990 where he won a European Cup winner's medal although he was largely a reserve for Marco van Basten.
He moved to Fiorentina for two seasons, then played for Pescara and Udinese. He won three caps for Italy.
"Thank you for everything you have taught all of us. Ciao, Stefano," wrote Real Madrid Carlo Ancelotti, one of Borgonovo's former team mates, on Twitter.