Cilic, who also won the tournament in 2009 and 2010, captured his ninth career title and improved his record to 17-4 in Zagreb.
"I felt I played an almost perfect match, for sure the best one in a year, year and a half," Cilic said. "Everything worked perfectly—serve, return, movement on court. ... I put big pressure on him."
Cilic converted four of 12 break points. He broke early for a 2-0 lead and again to lead 5-3 in the first set. Melzer won just one more game by the end of the match.
"He deserved the victory," said Melzer, whose record against Cilic dropped to 2-7. "It was a really good match he played—very well from the baseline, had good serve. I had to play for all points on my serve."