The Spaniard was at fault for the incident, taking too much of the kerb heading into the final corner, sending his car spinning around and off into the gravel, which failed to slow him down before a big impact with the barriers.
Strong winds and poor set up choices for some teams have wreaked havoc in Imola, where Red Bull and Max Verstappen are looking to bounce back following defeat last time out in Miami.
42-year-old Alonso walked away from the incident, but will be worried that it will have an impact on his weekend as a whole, having not been a feature so far alongside team-mate Lance Stroll.
FP3 got back underway after just four minutes at the Autodromo Enzo e Dino Ferrari circuit, following some quick work by marshals to get Alonso's car out the way and check the structure of the barriers at the final corner.