It was Wong's third win at the prestigious event after 1990s cult hits - Days of Being Wild, and Chungking Express.
"I am proud to be part of Hong Kong cinema," he said paying homage to his home in a brief media session after the glittering ceremony.
The action epic inspired by the life of kungfu master Yip Man secured accolades in most of the major categories, including best screenplay and best cinematography.
Chinese star Zhang Ziyi, was crowned best actress, for her performance as the daughter of a kungfu master who fell for Yip in the film.
"It was an uneasy journey. I have gained a lot [from the movie] for my own life," Zhang said on stage at the event at Hong Kong's Cultural Centre.
Last month, The Grandmaster snapped up seven awards at the Asian Film Awards in Macau.
The movie's production spanned several years and touched upon several decades of Chinese history as well as rivalry between various martial arts masters.
Yip, played by Hong Kong actor Tony Leung, was the mentor for legendary martial arts movie star Bruce Lee and is believed to have played a key role in shaping him during his childhood days.
The best actor award went to Nick Cheung for his role in action thriller Unbeatable as a former boxing champion who struggled to redeem himself in the ring.
Cheung beat Hong Kong actor Tony Leung Chiu-wai in the best actor category, who was nominated for playing the eponymous Grandmaster in Wong's piece.
"I didn't think I should get the awards necessarily as the competitors were very strong," Cheung told reporters at a press conference late Sunday.
The awards also saw low-budget dance feature The Way We Dance snap up three awards, including best new director for Adam Wong.
Together with Taiwan's Golden Horse Awards, the Hong Kong Film Awards ceremony is one of the Chinese film industry's most prestigious events.