The 68-year-old worked with Jackson throughout his career, including an appearance on the singer's Bad album in 1987.
And Jackson featured on the "Superstition" singer's album "Characters", with Wonder honouring the late singer at a tribute concert following his death in 2009.
When asked by TMZ about how people should feel about listening to his music, the "Isn't She Lovely" star suggested they should distinguish between Jackson and his legacy.
"He's died, he's dead," he insisted. "Hopefully, we can continue the legacy of inspiration he has given a lot of kids and a lot of people."
The Dan Reed-directed feature has been met with significant opposition, with the Jackson estate slamming the film as a "lurid production."
"This so-called 'documentary' is just another rehash of dated and discredited allegations," a statement to Entertainment Tonight read. "It's baffling why any credible filmmaker would involve himself with this project."
In the film, James Safechuck and Wade Robson make a string of allegations against the singer, claiming that he sexually abused them when they were young, shared the bed with them and even conducted a mock wedding ceremony with 10-year-old Safechuck.
Former child star Corey Feldman, who was pals with the "Thriller" hitmaker, has defended the singer, claiming that the two "shared common ground."
"What happened with me was strictly above board," he told Page Six. "We'd be on the phone for hours. You're talking about someone who has spent their life in the industry. We both came from abuse, abusive homes."
The film previously aired over two consecutive nights on the HBO network in the U.S. starting Sunday, March 03 and will air in the U.K. on Channel 4 on Wednesday.