Mr. Rajoy dissolved the parliament of Catalonia, which represents one-fifth of the Spanish economy, and called new elections in December, which served only to confirm the profound split in Catalan society. Mr. Puigdemont and other separatists retained their narrow parliamentary majority, with almost exactly the same share of votes — 47.5 percent — as two years earlier.

“It seems absolutely counterproductive to use criminal law and this court to solve a politico-constitutional conflict,” said José Antonio Martín Pallín, a former judge of the Supreme Court.

Since Friday’s court decision in Madrid, protesters have been back on the streets of Barcelona and other cities. Roger Torrent, the pro-independence speaker of the Catalan Parliament, is pushing for lawmakers to elect Mr. Puigdemont in absentia, though the former president has recently said he is no longer a candidate; opposition lawmakers want Mr. Torrent to resign, instead.

Separatist lawmakers have two months to form an administration or force new elections.

“Puigdemont’s arrest does not bridge the divisions between secessionist parties over what to do next,” Antonio Barroso, a political analyst at consulting firm Teneo Intelligence in London, wrote in a note on Monday.

The politics of Spain have also shifted: Mr. Rajoy now leads a minority government, and his center-right People’s Party finished last in the Catalan election. He risks being outflanked by a center-right party, Ciudadanos, that was founded on an anti-secession platform and won the most votes in Catalonia in December.

“One can be critical of the leaders on both sides and how they have handled every part of this conflict, but I don’t think this should be seen through the lens of a conflict between the rule of law and democracy,” said Alan Solomont, a former United States ambassador to Spain who is now dean of the Tisch College of Civic Life at Tufts University. The better lens, Mr. Solomont argued, was that “Catalonia is a region, subject to the Spanish Constitution of 1978, and a national government always has the right to enforce national law.”