Mr Moore provoked outrage when he said top-level women’s players rode “on the coattails of the men” and were “very, very lucky” to have equal prize money.
The tennis world reacted strongly. World number-one, Serena Williams, and all-time great Martina Navratilova rebuffed the statements and the ATP men’s tour formally denounced them.
Tournament owner Larry Ellison announced Mr Moore’s resignation and championed the sport’s efforts toward equality.
“Nearly half a century ago, Billie Jean King began her historic campaign for the equal treatment of women in tennis,” said Mr Ellison.
“What followed is an ongoing, multi-generational, progressive movement to treat women and men in sports equally.
"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.”
South African Mr Moore, 69, had also highlighted Canada’s Eugenie Bouchard, and Spaniard Garbine Muguruza as being among the “very attractive prospects” on the WTA circuit, before explaining that they were “physically attractive and competitively attractive”.
“If I was a lady player, I’d go down every night on my knees and thank God that Roger Federer and Rafa Nadal were born, because they have carried this sport,” he said.
The former ATP Tour player quickly offered an apology, but the damage had already been done. He had only taken over as tournament director late last year.
This is what Raymond Moore said female tennis players should be doing. pic.twitter.com/Cwa1E9e6zn— Sky News (@SkyNews) March 21, 2016