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1936–1939: Tracy collaborations and Gone with the Wind

Gable made three pictures with Spencer Tracy, which boosted Tracy's career and permanently cemented them in the public mind as a team. San Francisco (1936), with Jeanette MacDonald, featured Tracy for only 17 minutes in an Oscar -nominated portrayal of a Catholic priest who knocks Gable down in a boxing ring. The film was a box office hit and remains the third-highest-grossing film of Gable's career. Their next film together was the Academy Award–nominated box office success Test Pilot (1938), with Myrna Loy, who made seven pictures with Gable. He plays Jim Lane, the test pilot of the title; Tracy is his sidekick mechanic, Gunner Morse.

For their final film, 1940's Boom Town, Tracy would play a larger role, with billing directly under Gable and above Claudette Colbert and Hedy Lamarr. The picture, a lavish epic about two oil wildcatters who become partners then rivals, was a box office success, earning $5 million. Gable and Tracy were off-screen friends; Tracy was one of the few Hollywood industry luminaries who attended Lombard's private funeral. After Boom Town no more Gable-Tracy partnerships were possible; Tracy's success led to a new contract and both stars had conflicting stipulations requiring top billing in MGM movie credits and on promotional posters.

Despite his reluctance to play the role, Gable is best known for his Oscar-nominated performance in the Academy Award-winning best picture Gone with the Wind (1939). Carole Lombard may have been the first to suggest that he play Rhett Butler (and she play Scarlett) when she bought him a copy of the best-seller, which he refused to read. His total salary was $117,917 for the film ($ 2,582,890 in 2023).

Butler's last line in Gone with the Wind, " Frankly, my dear, I don't give a damn ", is one of the most famous lines in movie history. Gable was an almost immediate favorite for the role of Rhett with both the public and producer David O. Selznick. Since Selznick had no male stars under long-term contract, he needed to negotiate with another studio to borrow an actor. Gary Cooper was Selznick's first choice. When Cooper turned down the role of Butler, he was quoted as saying, " Gone With the Wind is going to be the biggest flop in Hollywood history. I'm glad it'll be Clark Gable who's falling flat on his nose, not me." By then, Selznick had become determined to hire Gable, and set about finding a way to borrow him from MGM. Gable was wary of potentially disappointing an audience that had decided that no one else could play the part. He later conceded, "I think I know now how a fly must react after being caught in a spider's web."

According to Lennie Bluett, an extra in the film, Gable almost walked off the set when he discovered the studio facilities were segregated and signage posted "White" and "Colored". Gable phoned the film's director Victor Fleming and told him, "If you don't get those signs down, you won't get your Rhett Butler." The signs were then taken down. Gable tried to boycott the Gone with the Wind premiere in segregated Atlanta, because African American actors Hattie McDaniel and Butterfly McQueen were not permitted to attend. He reportedly only went after McDaniel pleaded with him to go. They appeared in several more films, remaining life-long friends and he always attended her Hollywood parties.

Gable did not want to shed tears for the scene after Rhett inadvertently causes Scarlett to miscarry their second child. Olivia de Havilland made him cry, later commenting, "Oh, he would not do it. He would not! Victor (Fleming) tried everything with him. He tried to attack him on a professional level. We had done it without him weeping several times and then we had one last try. I said, 'You can do it, I know you can do it, and you will be wonderful...' Well, by heaven, just before the cameras rolled, you could see the tears come up at his eyes and he played the scene unforgettably well. He put his whole heart into it." The role was one of Gable's most layered performances and partially based on the personality of director and friend Fleming.

Years later, Gable said that whenever his career would start to fade, a re-release of Gone with the Wind would soon revive his popularity, and he continued as a top leading actor for the rest of his life. One reissue publicized "Clark Gable never tires of holding Vivien Leigh".