Ferrer had not planned to return this year but stood in at the last minute following world number one Rafael Nadal's withdrawal through injury.
The 31-year-old will climb to fourth in the world rankings on Monday, displacing Argentine Juan Martin del Porto who played in Rotterdam this week.
"This title was very important to me after seven finals without a victory," said Ferrer after claiming his 21st career win.
Fognini had won 10 matches in a row including helping Italy beat Argentina in the Davis Cup first round two weeks ago and victory in the Chilean ATP tournament at Vina del Mar last weekend.
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