In a gala ceremony held on Thursday in Kuala Lumpur, both the Asian Champions League MVP and Manchester United star were recognised as the continent's best players
The former Gamba Osaka man beat 2004 recipient Ali Karimi of Persepolis and Iran and Guangzhou Evergrande defender Zheng Zhi for the award, which has come in for criticism in previous years for its insistence 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 and 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 also received honours.
In the first category, created this year to recognise Asian players playing outside of the continent Japan, Manchester United superstar Shinji Kagawa saw off international team-mate Yuto Nagatomo as well as Australia's Mark Schwarzer.
Brazilian Rogerio de Assis Silva Coutinho of Kuwait SC was handed the Foreign Player of the Year award, beating fellow countrymen Bruno Correa of Sepaphan and Ricardo de Oliveira of the UAE's Al Jazira.
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