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.