Cilic fired eight aces and won all but eight of the 41 points on his serve in breezing past Melzer 6-3, 6-1, adding this year's Zagreb championship to his previous wins in 2009 and 2010.
It was the ninth career ATP Tour for the Croatian, who improved to 9-7 in championship tilts.
Melzer, meanwhile, fell to 4-8 for his career in finals and dropped to 2-7 against Cilic.
Florida bear attack: Black bear mauls woman's face
Toddler uninjured after being knocked over by Obama family dog