The Vini Fantini rider beat Borut Bozic (Vacansoleil) and Mathew Hayman (Team Sky) to the line in Waregem.
They were part of a 10-man group that formed in the final 25km of the race.
With 13 hills, including the Berendries/Valkenberg and Oude-Kwarement/Paterberg double-headers on the Flanders parcours at the end of the month, in the second half of the race, small lead groups regularly formed with Gert Steegmans and Australian Hayman a constant presence.
Hayman went solo with 40km to go and had a 40 second lead on the chase group, only to be caught by Gatto and Stijn Vandenbergh before the group swelled to 10 riders.
Britain's Ian Stannard attacked with 8km remaining but was hauled back in before Europcar's Tommy Voeckler made his move.
He opened up a 16 second advantage and was nine seconds ahead going under the Flamme Rouge but was caught metres from the finish line and had to settle for fifth as Gatto took his first win of the year.