We’re not giving up ... but it will require a different time and a different balance of political forces, Catalan Vice President Pere Aragones said in an interview last week.
The Spanish court also dropped European arrest warrants for five other Catalan pro-independence leaders living abroad.
Protesters were walking from Brandenburg Gate to the justice ministry, carrying banners that read "Free Puigdemont and the Catalan political prisoners" and "Spain is not a democracy".
German police had earlier arrested Puigdemont as he crossed the border with Denmark by car, responding to a European warrant issued by Spain.
Puigdemont, who lives in self-imposed exile in Belgium, had been visiting Finland since Thursday for talks with lawmakers.
Puigdemont has been due to leave Finland on Saturday afternoon, but his exact whereabouts were unknown.
Puigdemont says if he would have done anything differently, he would not have waited until the 27th to make the independence call.
During last year's secession crisis in the Spanish region, Vila, who was serving as Puigdemont's business minister, quit the day before Catalan lawmakers made a unilateral declaration of independence on October 27.