In a gala ceremony held on Thursday in Kuala Lumpur, both the Asian Champions League MVP and Manchester United star were recognized as the continent's best players
The former Gamba Osaka man beat out 2004 recipient Ali Karimi of Persepolis and Iran and Guangzhou Evergrande defender Zheng Zhi for the award, which has in past years come under criticism for its requirement that the nominees attend the ceremony in order to be eligible to win.
The 2012 Asian Champions League MVP had a prosperous year for Ulsan Hyundai, scoring four goals in his side's 12-match unbeaten campaign on the way to a 3-0 win over Saudi Arabia's Al Ahli in the final.
Lee also scored eight goals in domestic play for Ulsan, who finished fifth in the K-League, as well as five goals ans three assists in eight appearances for the South Korea national team.
In the first year of the ceremony's revised format, the AFC Asian International Player of the Year and AFC Foreign Player of the Year were also to receive honours.
In the first category, created this year to recognize Asian players playing outside of the continent Japan and Manchester United superstar Shinji Kagawa beat out team-mate Yuto Nagatomo as well as Australia's Mark Schwarzer.
Brazilian Rogerio de Assis Silva Coutinho of Kuwait SC was named Foreign Player of the Year award, beating out fellow countrymen Bruno Correa of Sepaphan and Ricardo de Oliveira of the UAE's Al Jazira.
South Korea's bronze medal-winning Mens Olympic Team was named the Asian Men's Team of the Year, while the silver-winning Nadeshiko Japan were named the Women's Team of the Year.
2012 AFC Awards
Member Association of the Year - Iran
Fair Play Association of the Year - Uzbekistan
Dream Asia Award - United Arab Emirates
Futsal Team of the Year - Japan National Team
Club of the Year - Ulsan Hyundai
Women's Player of the Year - Aya Miyama