Wilder was famous for playing Willy Wonka and starred in a number of films directed by Brooks.
They collaborated on Blazing Saddles, Young Frankenstein and The Producers.
The director tweeted: "One of the truly great talents of our time. He blessed every film we did with his magic & he blessed me with his friendship."
Willy Wonka star Gene Wilder dies
Obituary: Gene Wilder
Actor Billy Crystal described Wilder as "a giant of comedy," adding: "His legacy of films is inspiring. A true genius," while actor and musician Steve Martin said: "Goodbye, Gene Wilder. You were one of the great screen comedians. Original and surprising every time."
Wilder worked with Richard Pryor on four films - Silver Streak, Another You, Stir Crazy and See No Evil, Hear No Evil.
Rain Pryor, his daughter, told The Hollywood Reporter: "To watch the two of them together, there's not a magic that's been like that in a long time."
She added: "[My father] always said: 'That man's a genius, and he's a good man, that's for sure'."
Denise Nickerson, who played the role of Violet Beauregarde, one of the five children to win golden tickets to Willy Wonka's Chocolate Factory, also paid tribute. The film was based on Roald Dahl's children's book, Charlie and the Chocolate Factory.
She tweeted: "RIP Gene. You were so talented and kind-hearted. You will be sorely missed by so many. All of us have lost our Willy Wonka. Love, Violet."
Rusty Goffe, who also appeared in the film as an Oompa Looma, said: "Gene Wilder was one of the nicest if not the nicest actor I have ever worked with. A true star. Thank you Mr Wonka."
Julie Dawn Cole, who played Veruca Salt, told the BBC Wilder was "a very kind, endearing, and patient man".
"He had five kids who were probably high on sugar bouncing all over the set, he was just a joy to work with," she said.
"The joy was that as children we just kind of accepted him, so I can't say I was in awe of him at 12 but I suppose I'm more in awe now, [thinking] 'Wow, I really worked with that legend.'"
Sir Roger Moore, who also worked with Wilder, wrote: "RIP Gene Wilder. Only happy memories of making Sunday Lovers together."
A number of comedians also took to social media to pay tribute, citing Wilder as one of their biggest influences.
Peep Show actor Robert Webb said: "Oh boy, Gene Wilder. The vulnerability in his eyes & the rage in his perfect voice. Incredible comic actor."
David Baddiel tweeted: "There was a time in the 70s where you knew a film was a comic masterpiece because it starred Gene Wilder."
Leigh Francis, normally known as his alter-ego Keith Lemon, wrote: So sad to hear about Gene Wilder. One of my Heroes. Comedic wizard."
Other actors paying tribute included West Wing star Rob Lowe, who said: "Gene Wilder as one of my earliest heroes.
"Blazing Saddles, Willy Wonka, are clinics on comic acting. Sad to hear of his passing."
George Takei, best-known for playing Hikaru Sulu in Star Trek, tweeted: "He was always able to make us smile, and that is no small feat. Rest with the stars, Gene Wilder."
Russell Crowe wrote: I saw Blazing Saddles seven times at the cinema with my school friends . George St. Cows outside. Gene Wilder you were a genius."
Veep star Julia Louis Dreyfus described Wilder as "wonderful", adding: "What an influence you were in my life. Thank you for all that joy."
Comic actress Sarah Silverman posted: Hilarious & heartbreaking in the very same moment. RIP beautiful Gene Wilder. There was & will never be anyone like you."