The world No.1's comments came after Indian Wells chief executive Raymond Moore sparked outrage by remarking on Sunday that women players ride on the coat-tails of the men. Moore later apologised but resigned from his position on Tuesday.
Murray believes "there should be equal pay, 100 percent, at all combined events", while Williams, a 21-times Grand Slam winner, has urged Djokovic to explain his stance.
"It has been disappointing," Williams, speaking to reporters at the Miami Open, said of the sexism row that has engulfed tennis.
"If I have a daughter who plays tennis and also have a son that plays tennis, I wouldn't say that my son deserves more because he is a man. If they both started at three years old I would say they both deserve the same amount of money.
"I have been playing since the age of two and it would be shocking to say my son would deserve more than my daughter. It is irrelevant.
"Novak is entitled to his opinion but if he has a daughter -- I think he has a son right now [17-month-old Stefan] -- he should talk to her and tell her how his son deserves more money because he is a boy.
"It all boils down to that. I would never put a sex against another sex. It's unfair to compare, we have had so many great women champions and players who have brought such great vision to the sport.
"There have been great men players too, but women's tennis is the biggest sport for women -- period.
"Men's tennis is not the biggest sport for them but it's still huge. You do have soccer, football, basketball. Everyone works really hard. Once again, it all boils down to how you'd explain it to your kids."
Djokovic, following his men's final victory over Milos Raonic at Indian Wells, said the men's tour should be more highly rewarded than the women's for attracting more spectators and greater viewing figures.
His stance has since been criticised by nine-time Wimbledon champion Martina Navratilova, and world No.2 Murray has also questioned his long-time rival's opinion, while appearing to take a dig at Ukrainian player Sergiy Stakhovsky, who opposes equal pay.
"Everyone is entitled to their own opinion and can have different views," said Murray.
"One of the things Novak said was that if women are selling more seats and tickets they should make more but at a tournament like this, for example, if Serena is playing on centre court and you have a men's match with Stakhovsky playing, people are coming to watch Serena.
"The crowds are coming to watch the women as well. The whole thing just doesn't stack up -- it changes on a day-to‑day basis depending on the matches you get.
"Men's tennis has been lucky over the last nine or 10 years with the players they've had, the rivalries which have come out of that. That's great but the whole of tennis should capitalise on that -- not just the men's game."
Murray was also baffled at the timing of Moore's original comments, ahead of what was an entertaining Indian Wells final with Victoria Azarenka beating Williams 6-4, 6-4.
"The timing of it [Moore's remarks] was just so strange, right before a great women's final, there were 16,000 people in the stadium waiting to see them play," added Murray.
"The whole thing was very strange and very disappointing. I don't understand at all where he was coming from at all with those comments. It made no sense at all."