The threats of a pounds 100,000 fine and having to play two matches behind closed doors are suspended for two years, while the deduction of three League points hangs over them until December.
The commission praised the off-field advances the club had made and the level of facilities. But they found the club guilty of misconduct through its failure to control their fans after two pitch invasions held up play for 32 minutes, and the Derby players, Martin Taylor and Paul Williams, were attacked as they fled to the dressing-rooms.
They also said the club had been instructed to give immediate attention to certain areas of match-day management, including picketing, entry to the stadium and movement of spectators within it.
The three-man commission, comprising the Challenge Cup committee chairman, Gordon McKeag, the Norwich chairman, Robert Chase, and the Cheshire FA Council representative, Alan Burbidge, toured the club's south London ground and took evidence from match officials, police, an FA crowd control observer, a representative from the Football Licencing Authority and the club itself.
David Bloomfield, an FA spokesman, said the suspended sentences would be imposed, in part or in full, in the event of serious misconduct involving Millwall or its supporters, either at home or away.
Millwall's chairman, Reg Burr, was not immediately available for comment. Chief Superintendent Ken Chapman, who was in charge of policing the match, said the commission had taken account of the efforts made to solve the hooliganism problem.
'They recognised what has been done by the police and everybody else to locate the criminals and those responsible,' he said.
'Under the guise of the tense situation, people decided to cause criminality.'