Mr Puigdemont, who is wanted in Spain for sedition and rebellion, was detained by German police acting on a European arrest warrant.
He will appear before a German judge later on Monday.
Clashes between protesters and police in Catalonia left at least 89 people injured and four arrests were made.
Mr Puigdemont was detained while crossing from Denmark on his way to Belgium, where he has been living in self-imposed exile since Catalonia's parliament unilaterally declared independence from Spain in October.
A European warrant for his arrest was reissued on Friday.
