Lord Glennie ruled an SFA judicial panel and appeal tribunal had acted outside their powers by handing a 12-month transfer ban to Rangers and proposed the matter be considered again by the second SFA tribunal.
Under SFA rules, Rangers could face a £100,000 fine, ejection from the Scottish Cup while the appeals panel could decide to suspend or terminate their membership of the SFA.
The SFA were disappointed with the club's decision to take the matter to court and, although they were given 21 days to appeal against the decision, they will follow the judge's suggestion.
An SFA statement read: "Football must always operate within the law of the land. Nonetheless, it is regrettable that a member club has sought recourse for a football disciplinary matter through increasingly costly civil court action.
"The right of appeal is now open to the Scottish FA through the Court of Session.
"However, by so doing, the very principles on which the Scottish FA - and, for that matter, UEFA and FIFA - are founded, namely football disciplinary matters being dealt with within its own jurisdiction, would be fundamentally compromised.
"Therefore, it is our intention to accede to Lord Glennie's request and refer the matter back to the appellate tribunal, which will consider the remaining sanctions open to it.
"Details of a new hearing date will be confirmed in early course."