"Nearly half a century ago, Billie Jean King began her historic campaign for the equal treatment of women in tennis," Ellison said. "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."
Among his comments, the 69-year-old South African 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.
When reaction to his remarks flooded in, the former ATP Tour player quickly offered an apology but the damage had already been done.
Moore had only taken over as tournament director late last year when Steve Simon resigned to become chief executive of the WTA Tour.
"I would like to personally thank all the great women athletes who fought so hard for so many years in the pursuit of equal prize money in professional tennis," Ellison added.
"All of us here at the BNP Paribas Open promise to continue working with everyone to make tennis a better sport for everybody."