Lee shared the news on his Instagram and Facebook accounts on Saturday (24Sep16), hours after Nunn had passed away in his hometown of Pittsburgh, Pennsylvania.
Nunn's wife Donna later confirmed to The Associated Press he had been battling cancer.
Bill and Spike collaborated on many projects, but it was the actor's role as Radio Raheem in Do the Right Thing which was his most notable character.
Raheem was the enduring neighbourhood figure who travelled everywhere with a boombox blasting Public Enemy's hit Fight The Power. Sporting brass knuckle rings reading 'Love' and 'Hate', he is choked to death by police, leading to a riot.
"My Dear Friend, My Dear Morehouse (College) Brother," Lee wrote on Saturday. "Da Great Actor Bill Nunn As Most Of You Know Him As Radio Raheem Passed Away This Morning In His Hometown Of Pittsburgh.
"Long Live Bill NUNN. RADIO RAHEEM Is Now RESTING IN POWER. RADIO RAHEEM WILL ALWAYS BE FIGHTING DA POWERS DAT BE. MAY GOD WATCH OVER BILL NUNN (sic)."
Nunn's first feature film was in 1988's School Daze alongside Lee, who would later direct the actor in Do The Right Thing. He went on to star opposite Whoopi Goldberg in 1992's Sister Act, and later featured in Sam Raimi's Spider-Man trilogy as Joseph 'Robbie' Robertson of The Daily Bugle newspaper.
Nunn last appeared onscreen as Cash in the TV series Sirens in 2014 and 2015.
In an interview in 2013, Bill remembered how Spike had originally offered him the role of DJ Mister Señor Love Daddy in Do The Right Thing, a part that later went to Samuel L Jackson.
"Spike said, 'Hey, I want you to do this,'" Nunn recalled. "He had me in mind to do Mister Señor Love Daddy at the time, the DJ character. But I'm so glad it worked out the way it did.
"Radio Raheem was really good for me because I like those characters that don't have a lot of lines but they're kind of significant to the story," he explained.
Hollywood stars took to Twitter on Saturday to pay tribute to the actor, after Lee broke the news of his death.
"Rest in peace Bill Nunn. Radio Raheem... Indelible," wrote Alec Baldwin, while Chris Rock simply posted, "RIP. Bill Nunn."
Samuel L. Jackson paid tribute to the "loved" actor. "RIP Bill Nunn!! Most Loved, Most Cherished!!" he wrote.
Denis Leary, who co-created the TV comedy series Sirens, added on Twitter, "Terrible news: the brilliant actor and one of my funniest friends Bill Nunn has passed. A monumental talent. #RadioRaheem #TheJob #SirensUSA."
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