Players from both sides were involved in a tunnel bust-up following Leeds' 3-2 win at Elland Road in February, which was sealed by Luciano Becchio's winner deep in time added on.
Doncaster have also accepted the same charge and have requested a personal hearing.
A brief Leeds statement read: "Leeds United have pleaded guilty to an FA charge of misconduct following the game against Doncaster Rovers at Elland Road last February. The club has not requested a personal hearing."
West Yorkshire Police launched an investigation into the incident, that occurred on the same day as Neil Warnock's appointment as manager, but no criminal proceedings were brought.