The 69-year-old South African had earlier told reporters that top-level women's players rode "on the coattails of the men", did not make any decisions and were "very, very lucky" to have equal prize money, sparking a firestorm on social media.
He also said that, "if I were a lady player, I would go down every night on my knees and thank God that Roger Federer and Rafael Nadal were born. They have carried the sport."
Moore also singled out Canada's Eugenie Bouchard and Spaniard Garbine Muguruza as being among the "very attractive prospects" on the WTA circuit tour, before explaining that they were "physically attractive and competitively attractive".
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Serena Williams, when asked in her post-match news conference about Moore's comments, replied: "Those remarks are very much mistaken and very, very, very inaccurate...
"Obviously I don't think any woman should be down on their knees thanking anybody like that."
Asked if people had interpreted Moore's words harshly, Serena scoffed.
"If you read the transcript you can only interpret it one way. I speak very good English. I'm sure he does to," she said.
Moore later apologised in a statement which he issued later in the day: "At my morning breakfast with the media, I made comments about the WTA that were in extremely poor taste and erroneous.
"I am truly sorry for those remarks, and apologise to all the players and WTA as a whole.
"We had a women's final today that reflects the strength of the players, especially Serena and Victoria, and the entire WTA. Again, I am truly sorry for my remarks."
Moore, a former ATP Tour player who won eight doubles titles during the 1970s and early 1980s, issued his apology after former world number one Victoria Azarenka had beaten an error-prone Serena 6-4 6-4 in the women's final.
Moore landed himself in hot water when he said during his annual breakfast with media covering the Indian Wells event: "You know, 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. 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."
Moore went on to say that Muguruza and Bouchard were among a "handful of very attractive prospects" who could take up the mantle in the women's game.
When asked what he meant by attractive, he replied: "They are physically attractive and competitively attractive. They can assume the mantle of leadership once Serena decides to stop."
Billie Jean King, who co-founded the WTA Tour and has long been a pioneer in the women's game, tweeted: "Disappointed in #RaymondMoore comments. He is wrong on so many levels. Every player, especially the top players, contribute to our success."
Fellow American Chris Evert, an 18-time grand slam champion, tweeted: "Now is the Golden Era 4 men, no doubt, but women have worked, fought harder, and have been bigger draws many times."
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