Molinari survived a playoff against Sweden's Robert Karlsson, the pair separating themselves from the field by six shots, before Molinari birdied the second extra hole to take the title.
Molinari, who won the US Amateur Championship inÃ‚Â 2005, has been in dominating form on the European Challenge Tour this season winning three times, easily winning the money list there and earning his full European Tour playing rights in 2010.
Edoardo's brother, Francesco, has also had his best season in professional golf in 2009. He was in 12th position in the Race to Dubai standings prior to this the Dubai Championship.
Karlsson has spent much of this season on the sidelines with an eye injury and so this represents and encouraging return to the sort of form that saw him record a superb season in 2008. Karlsson took three months away from the game in the middle of this season.
Hirofumi Miyase and Ireland's Shane Lowry finished in a share of third while New Zealander Eddie Lee tied for 5th with Tadahiro Takayama.
Steve Conran was the leading Australian finishing in a share of 7th, Wayne Perske was 52nd and Paul Sheehan 459th.
The Japan Golf Tour now plays the Casio World Open.
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