Klaus Armstrong-Braun, the only Green councillor in the 70-member council, challenged the order saying it caused serious problems for sole representatives.
The order was overturned by three appeal court judges, who ruled its democratic implications had not been considered.
Lord Justice Schiemann said: 'It must be enormously tempting to close out opponents and to do so in the conviction that the moving of a motion by a lone councillor would waste everybody's time.'
The council was refused leave to appeal to the House of Lords, but could petition the Law Lords directly for an appeal hearing.
Flintshire claimed the court had confirmed its ability to make such a standing order: 'The court identified a technical flaw and on that basis alone made its decision.'