At least 92 people were confirmed injured in clashes out of a total of 465 who went to hospital, emergency services said, as police cracked down on a vote the Spanish central government branded a "farce".
The violence further heightened tensions between the national government of Prime Minister Mariano Rajoy and the authorities in Catalonia in the worst political crisis in Spain in decades.
The vote was organised in secret under the threat of reprisals and criminal charges but thousands of Catalans stood in defiance of the central government crying "Votarem" -- "We will vote".
"They took the ballot boxes by force... and they literally yanked them from us as we continued to sing 'Els Segadors', the Catalan hymn, and shouting "long live democracy'," said Marc Carrasco, in charge of one of the Barcelona polling stations.
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In the second such vote in three years, more than 5.3 million people were called on to have their say on independence from Spain in the wealthy northeastern region which has its own distinct language and culture.
The referendum law foresees a declaration of independence within 48 hours of a 'Yes' vote but it remains unclear what the regional government will actually do so.
The vote has been deemed unconstitutional by Madrid and the courts, with judicial officials ordering police to seize ballot papers, detain key organisers and shut down websites promoting the referendum.
Deputy Prime Minister Soraya Saenz de Santamaria called on the Catalan government to call off what she dismissed as a "farce".
The Catalan government has "behaved in an absolutely irresponsible manner, it tried to annul law and justice in Catalonia, and with it democracy," she said.
In central Barcelona, riot police charged at demonstrators who were sitting on the ground at a polling station, and fired rubber bullets, witnesses said.
The crackdown drew a sharp rebuke from Catalan leaders and others including Nicola Sturgeon, leader of the pro- independence Scottish National Party.
"The unjustified use of violence, which is both irrational and irresponsible, by the Spanish state will not stop the will of the Catalan people," Catalan president Carles Puigdemont said.
"The head of a cowardly government has flooded our city with police," Barcelona Mayor Ada Colau wrote on Twitter, adding: "Barcelona city of peace, we are not afraid" -- a slogan coined after August's jihadist vehicle rampage that killed 16 people.
Riot police also stormed a polling station near Girona, smashing the glass doors of the sports centre where Puigdemont was due to vote and cutting a chain to force their way in.
But the regional government said Puigdemont had managed to vote anyway in nearby Cornella del Terri, and in several areas voting was reported to be peaceful.
The trouble caused Barcelona football club to play its La Liga tie against Las Palmas behind closed doors after the Spanish league refused to postpone the match.
Under a sea of umbrellas outside a school in Barcelona, a crowd gathered, among them elderly people in wheelchairs, families with buggies and parents clutching toddlers by the hand. With no police in sight, they were able to cast their ballots, prompting scenes of jubilation.
"That's the great hope, to be able to vote freely like this despite the problems we've faced, I'm very happy. I can die peacefully," added Jose Mas Ribas, 79.
Although Catalans are divided over independence, most want to vote on the matter in a legal and binding plebiscite.
Pro-separatist lawmakers in Catalonia have pushed for a referendum since September 2015 when they won a narrow majority in the region's parliament.
Although Catalonia already has significant control over education, healthcare and welfare, the region says it pays more in taxes than it receives from Madrid.
Rajoy's government has come under fire for limiting its response to the crisis, and several leftwing politicians called today for him to resign.
"The state needs to explain the benefits of remaining united, instead of repeating all the time that the referendum is illegal," said Rafael Castillo, a 59-year-old engineer at a Madrid rally, wearing a scarf with the Spanish flag around his neck.
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