Youzhny, meeting Spain's Ferrer in a final for the first time, notched a 6-3, 7-5 triumph for his second title of the year and 10th of his career.
The Russian, who also won at Gstaad this year, improved to 5-3 all-time against the world No. 3 in their first meeting since the third round of the 2012 French Open.
Ferrer, meanwhile, was seeking this third title of 2013. He instead dropped to 2-6 in finals after also falling at Acapulco, Miami, Portugal, Stockholm and the French Open.
He corralled victories at Auckland and Buenos Aires early in the season.
Swim Week Miami Beach 2014 [PHOTOS]