Emergency services said 24 people were lightly injured in clashes between police and demonstrators.
The second round of a vote on Jordi Turull's candidacy for head of the Catalan government has been canceled since the candidate is detained and can not show up in the parliament in person, speaker of the Catalan parliament Roger Torrent said.
Turull was one of the five politicians who responded to a court summons, only to find that Judge Llarena had chose to send them to jail, denying them bail.
Announcing the rebellion charges, which carry a maximum sentence of 30 years' imprisonment, Llarena said Catalan separatist politicians and grassroots groups had "colluded" for the past six years to draw up a plan for regional independence in defiance of Spain's legal and constitutional order.
Llarena also issued global arrest warrants for former Catalan President Carles Puigdemont, who is in self-imposed exile in Belgium along with four of his former ministers.
However, on Friday, Llarena issued fresh orders for European and worldwide arrest warrants for Catalan politicians overseas, including Puigdemont and Rovira. "It is not right for a judge to do politics", Mr Puigdemont said.
The central government has been running Catalonia from Madrid since snatching away Catalonia's regional powers over the October breakaway vote, which courts have ruled unconstitutional.
The decision sparked a wave of demonstrations in Barcelona and across Catalonia on Friday.
The court did not give a date for the trial.
Although the leadership vote for Mr Turull can no longer take place on Saturday, Catalan parliament speaker Roger Torrent said he would use the parliamentary session to read a statement in support of those in prison.
The judge later ruled that Turull and four others - among them the former speaker of the Catalan parliament - would be denied bail and remanded in custody. She said: "I start a hard road, that of exile", and is believed to be in Switzerland where Anna Gabriel is now living.
The central government is now running Catalonia from Madrid.
But the separatist majority proved to be a failure in electing a regional government in a Thursday vote.
Spanish Prime Minister Mariano Rajoy had in December called for snap elections in Catalonia.
That harsh judgment led crowds of protesters to gather around Spanish government buildings in Barcelona as well as other parts of the region.
The court's decision will likely put an end to a planned vote this Saturday at the Catalan regional parliament to pick a new leader after Mr Puigdemont's departure past year.
But they have still not been able to form a government as their two previous candidates for the presidency proved problematic.