On social media, Catalonians likened the detention of Mr Puigdemont to the arrest of leftist Catalan president Lluis Companys by the Gestapo. In videos posted on a Spanish news website, police used their batons and appeared to fire warning shots.
Many chanted "no more smiles", a reference to the longstanding claim from Catalan separatist leaders that their drive to break the wealthy northeastern region away from Spain would be a "revolution of smiles".
German police said they had arrested Mr Puigdemont in the northern state of Schleswig-Holstein.
Llarena ruled that a total of 25 Catalan separatists would be tried for rebellion, embezzlement or disobedience.
Puigdemont is wanted in Spain for sedition and rebellion for organising an illegal referendum - charges which carry up to 25 years imprisonment.
Despite the efforts of Puigdemont, who fled to Brussels after the Catalan parliament declared independence on October 27 and Madrid countered by taking control of the region, no European Union member state backed the secessionist cause.
Catalonia will remain under direct rule by Madrid as long as it fails to form a new government. Puigdemont had been visiting Finland since Thursday, but slipped out of the Nordic country before Finnish police could detain him.
His lawyer, James Alonso-Cuevillas, confirmed the arrest on Twitter.
"The president was going to Belgium to put himself, as always, at the disposal of Belgian justice", Pique said.
Puigdemont's supporters, however, lamented his capture and said they hoped Germany won't honour Spain's extradition request.
Elsa Artadi, a spokeswoman for Puigdemont's Together for Catalonia party, said that he should fight his extradition to Spain.
"What they are doing these days is totally disproportionate, we are being treated like criminals for wanting independence", Rosa Vela, a 60-year-old teacher, told AFP.
Catalonia's deposed leader Carles Puigdemont: "I will not throw in the towel. Trying to destroy a European democracy, bypassing democratic laws, breaking up coexistence or misusing public money can not enjoy impunity".
Thousands of Catalan separatists hit the streets of Barcelona on Sunday, vowing the arrest of former Catalan president Carles Puigdemont in Germany would not stop their push for independence.