ATP president Chris Kermode will not have his contract extended, after all three players' representatives on the board voted against him.
Rafael Nadal warned on Wednesday that a change at the top will "stop the process of improving the sport".
But a board meeting in Indian Wells chose not offer the Briton, 54, a new deal when his second three-year term expires at the end of this year.
The 10 ATP Player Council members were split when they discussed the issue.
But their representatives on the board - the former player Justin Gimelstob, the TV executive David Egdes and the British lawyer Alex Inglot - all voted against an extension.
Gimelstob has remained on the board while facing a continuing legal case, having pleaded not guilty to a charge of battery causing serious bodily injury in Los Angeles in October.
The world number one Novak Djokovic is the president of the Player Council, and widely considered to have been one of the chief agitators for change.
But at a news conference in Indian Wells on Thursday, Djokovic refused - despite repeated questioning - to say whether he supported the decision to oust Kermode.
"I will not answer your question directly," Djokovic said.
"I will not express my personal views on that. By sharing that information, I expose myself and I become liable to breach of confidentiality within the structure, so I'm not willing to risk that.
"We have the inaugural ATP Cup in 2020, we have the Next Gen Finals - there are a lot of positives, without a doubt. But also there's a lot of things that are happening internally that need a lot of addressing."
Djokovic said the members of the council "talked to a large number of players" to establish their views, but added that he did not talk personally to either Nadal or Roger Federer.
He said: "It goes both ways, right. If they wanted to talk about something, they could also approach, and talk about something. We've been elected by Federer, Nadal and everyone else to be representing players' best interests."
In a statement, the ATP said Kermode's tenure has seen "record prize money and commercial growth for the organisation, while attendance and viewership of the ATP Tour has soared".
It added: "Kermode's vision and leadership since 2014 has been instrumental in the creation of landmark new ATP events such as the award-winning Next Gen ATP Finals in Milan, as well as the upcoming ATP Cup in 2020."
Kermode himself said: "It's been a privilege to serve as ATP executive chairman and president since 2014 and I'm very proud of what we have achieved during this time.
"I would like to thank everyone at the ATP, and all the players and tournaments for the support over the years. I remain fully dedicated to the role for the remainder of my term and wish the organisation every success in the future."