Cruyff, one of the finest players to grace the game, publicly clashed with the other four commissioners on Ajax's supervisory board after they named former coach Louis van Gaal, Danny Blind and Martin Sturkenboom as directors but kept him in the dark.
Cruyff earlier this week said he was taking legal action against the commissioners over the directors' appointment and had challenged the members council to pick a side.
The 24-man members council instead opted to support neither side, saying they had lost faith in any further cooperation between them.
"This board could not continue and therefore we made this choice," members council chairman Rob Been Jr. told reporters.
"Now we choose an interim board of three members, who will vote for the club at the shareholders meeting on December 12 and after that we will form a council of members, who will appoint a new board of commissioners.
"But none of the five members of the recent board will return as commissioner in the new board."
At the heart of the dispute has been Cruyff's thorny relations with Van Gaal, who coached Ajax to their last European Cup triumph 16 years ago and was sacked as Bayern Munich manager in April.
Cruyff had not wanted to work with Van Gaal, who himself would have been unwilling to adopt the Dutch great's technical blueprint for the development of Ajax and the club's young players.
The shareholders meeting will decide the club's future direction but Been and fellow board member Keje Molenaar said the members still supported Cruyff's technical blueprint and that the technical structure of the club was not on the agenda for Monday's meeting.
"We will stay on that track," Molenaar told NOS-TV.
