FIFA's Executive Committee passed a resolution calling on all members to respect the statute which bans them from taking football-related cases to the civil court.
"The structure of organised football is in danger if clubs and players do not respect the statutes of FIFA, the confederations and the associations," said the resolution.
"Organised football of FIFA would no longer be possible if every club or player went to a local court when they disagreed with decisions which became final and binding."
Sion were kicked out of the Europa League by UEFA for fielding ineligible players in a play-off tie but later won an injunction at a civil court in Switzerland ordering their reinstatement.
On Wednesday, UEFA President Michel Platini and General Secretary Gianni Infantino appeared before a prosecutor in the Vaud canton tribunal to explain why the order had not yet been implemented.
UEFA have appealed to Sion to settle the case at the Court of Arbitration for Sport (CAS) which is recognised as sport's highest tribunal, rather the proceeding with the civil case.
Sion signed six players in the summer despite being subject to a transfer ban after being found guilty of inducing an Egyptian goalkeeper to break his contract with his previous club to join them in 2008.
FIFA added in its resolution that this decision "was confirmed by the independent international Court of Arbitration for Sport (CAS) and the Federal Supreme Court of Switzerland."
The six players were initially banned from playing in the Swiss League, which backed down when they won the right to play in a civil court.
But, in another twist on Wednesday, the SFL handed each of the six players five-match bans for breaking its statutes by taking their case to the civil court.
