The Frenchman took the event for the third time, after winning the tournament in 2007 and 2008.
Fognini, playing in his first ATP World Tour final, made a determined start and broke early for a 2-0 lead before Simon recovered to make it 2-2.
Simon broke again to lead 3-2, but immediately lost his serve in a game where both players made several forays to the net.
At 3-3, Simon broke for the third time and held on to take the set, despite an apparent eye injury.
The second set was dominated by several long rallies, but Simon seemed more in control and at 2-2 broke to take the lead. Leading 5-3, Simon trailed 40-0 on Fognini's serve before rallying to win the match.