The 31-year-old Ognenovski led his South Korean club Seongnam Ilhwa to victory in the Asian Champions League final in Japan this month.
"To be named in the initial list of 15 players itself was a big honour. To win the award was unbelievable and humbling," Ognenovksi said.
Leading AFC players including Korean Park Ji-sung, Australian Tim Cahill and Japanese Keisuke Honda were ruled out of contention for the award by an eligibility rule which states that only players attending the Kuala Lumpur ceremony can win.
Seongnam Ilhwa won the club team of the year award, Japan were named Asia's top international men's side after reaching the last 16 in the World Cup and Australia took the women's prize.
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