Tournament owner Larry Ellison said in a statement that Raymond Moore was quitting as chief executive officer and tournament director of the USD 7 million event featuring men's and women's players in the California desert.
Moore informed Ellison of his decision when they spoke earlier in the day.
"Ray let me know that he has decided to step down from his roles as CEO and tournament director effective immediately," Ellison said. "I fully understand his decision."
Moore apologized after he was roundly criticized by executives from the women's and men's pro tours, players Serena Williams and Victoria Azarenka and on social media for his comments Sunday.
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The 69-year-old former touring pro from South Africa has been CEO of the tournament since 2012. In the event's early years, Moore and fellow ex-player Charlie Pasarell started PM Sports Management, which oversaw the tournament as it expanded.
"In my next life when I come back I want to be someone in the WTA because they ride on the coattails of the men. They don't make any decisions and they are lucky. They are very, very lucky," Moore said.
He also referred to women's players as "physically attractive and competitively attractive." Moore later apologized, calling his comments "in extremely poor taste and erroneous."
Moore clearly had no intention to leave his post based on comments he made to reporters Sunday on the last day of the two-week tournament. Before the backlash over his controversial comments began, he was asked how long he planned to remain in charge.
"Firstly, I love what I'm doing. I'm passionate about it. I enjoy it," Moore said. "Who knows who the face of the tournament will be down the road. But I don't think that, oh, I'm going to stop next year or three years."
"I'm proud to say that it is now a decade-long tradition at our tournament at Indian Wells, and all the major tennis tournaments, to pay equal prize money to both the women and the men," Ellison said in his statement.
Ellison thanked the "great women athletes" who fought so hard in pursuit of equal prize money in pro tennis.
"All of us here at the BNP Paribas Open promise to continue working with everyone to make tennis a better sport for everybody," he said.