The 85-page appeal, seen by AFP on Monday, asks that the Supreme Court's "actions" be declared "null" 10 days after Judge Pablo Llarena said 25 Catalan separatist leaders -- including Puigdemont -- would be prosecuted over the region's secession bid last October.
In the appeal, Puigdemont's lawyer Jaume Alonso-Cuevillas demands that the court drop the charges of rebellion and misuse of public funds against Puigdemont and another of his clients -- former regional minister Clara Ponsati.
Both fled Spain for Belgium after the failed independence push. Ponsati then left for Scotland where she was detained after Spain issued European arrest warrants against fugitive separatist leaders, and freed on bail.
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Alonso-Cuevillas also wants the court to drop charges of misuse of public funds and disobedience against another client, former regional minister Lluis Puig.
The appeal states that under Spanish law, the rebellion offence, which can fetch up to 30 years in prison, implies there was a violent uprising.
But it maintains that if there was any violence before or on October 1st, the day when an independence referendum was held in Catalonia despite a court ban, it was "isolated" and did not justify the rebellion offence.
In his finding, Judge Llarena pointed to Puigdemont's refusal to call off the referendum despite police warning of a "grave risk of violent incidents."
Some 60 policemen were hurt trying to stop the vote, the judge noted, without mention of the attacks by police against voters waiting outside polling booths.
Puigdemont was arrested by German highway police late last month just days after the arrest warrant was issued, as he was travelling from Finland back to Belgium, where he has been living in self-imposed exile since Catalonia's failed independence bid.
German judges have ordered Puigdemont to remain in custody in the northern town of Neumuenster as they mull Spain's request for him to be handed over.