Fifth-seeded Cilic gained his fourth title in Zagreb and became the third Croat overall to win at least 10 career titles. Cilic also lifted his career record in Zagreb to 22-4, winning 20 of his last 21 matches at the event.
Cilic -- champion here in 2009, '10 and last year -- struggled with his first serve in the opening set but played some great returns with a solid baseline performance.
The 35-year-old Haas broke in the first game but then lost five out of the next six. Haas also wasted a break point for a 4-2 lead in the second set, allowing Cilic to step up the pressure and gain a 5-3 lead.
Haas saved a match point, but Cilic made sure he used the second opportunity.
"It's nice to be in the finals after the tough last year I had," Cilic said. "I played (under) great pressure."
Haas in turn said Marin "played big points better."
Cilic's coach Goran Ivanisevic has 22 titles and Ivan Ljubicic has 10.
Cilic and Haas are tied 2-2 in head-to-heads.
Making the Zagreb final was Haas' best performance this year, after he lost in the opening rounds in Auckland and at the Australian Open. Haas won his last title in Vienna last year.