Cilic dominated from the start and did not give the fourth-seeded Melzer, who has now beaten the Croatian only twice in nine meetings, a chance to turn the score in his favour.
"This final is probably the best match I played in this season," Cilic said.
"This was an almost brilliant match on my part. It was tough to break Melzer in the first set, but after I did it the path to victory was open."
Cilic had previously won in Zagreb in 2009 and 2010.
"Cilic was much better today and deserved to win in front of his own crowd," Melzer said.