WTA chief executive Steve Simon said the umpire showed Williams a different level of tolerance over Saturday's outbursts than if she had been a man, BBC Sport reported.
She got a code violation for coaching, a penalty point for racquet abuse and a game penalty for calling the umpire a "thief" in the defeat by Naomi Osaka.
The American said it was "sexist" to have been penalized a game.
"The WTA believes that there should be no difference in the standards of tolerance provided to the emotions expressed by men versus women," Simon said in a statement.
"We do not believe that this was done last night."
He also called for coaching to be allowed "across the sport". Umpire Carlos Ramos penalized Williams after seeing her coach, Patrick Mouratoglou, making a hand gesture. The Frenchman later admitted he was trying to coach his player.
The head of the United States Tennis Association (USTA), which organizes the US Open, said men "are badgering the umpire on the changeovers and nothing happens".
"We watch the guys do this all the time," USTA chief Katrina Adams said.
"There's no equality when it comes to what the men are doing to the chair umpires and what the women are doing, and I think there has to be some consistency across the board.
"I'm all about gender equality and I think when you look at that situation these are conversations that will be imposed in the next weeks. We have to treat each other fairly and the same."
Williams, 36, was fined $17,000 (£13,100) for code violations that included calling Ramos a "liar" and "thief". She earned $1.85 million (£1.43m) in prize money for reaching the final.