Puigdemont "was arrested today at 11:19 am by Schleswig-Holstein’s highway patrol force," a German police spokesman told AFP, adding that the detention was based on a European warrant.
"He is now in police custody," added the spokesman.
Puigdemont’s arrest came just two days after Spain’s supreme court said it would prosecute for "rebellion" 13 Catalan separatists, including Puigdemont and his nominated successor Jordi Turull, over their role in the region’s failed breakaway bid. If found guilty, they face up to 30 years in prison.
Jordi Turull was detained on Friday along with five other leaders, sparking protests and clashes with police in Barcelona.
Issuing an international arrest warrant for Puigdemont on Friday, Judge Pablo Llarena accused the ousted Catalan leader of organising the independence referendum in October last year despite a ban from Madrid and "grave risk of violent incidents".
Puigdemont and four other deputies had fled to Belgium following their proclamation of independence for Catalonia in October, which sank the state into a crisis.
Spanish authorities have since imposed direct rule over the region, suspending the wealthy state’s autonomy over the last five months.
While separatist parties won Catalonia’s regional elections in December called by Madrid, they have been unable to form a government for the region as numerous leaders are in exile abroad or in jail.
Puigdemont himself had said from Belgium in early March that he was abandoning his bid to return as regional president, even though he had run in December’s polls from abroad.