In a press briefing, regional government spokesman Jordi Turull said 2.02 million Catalans voted "yes" to the question: "Do you want Catalonia to become an independent state in the form of a republic?"
He added 2.26 million people took part.
Catalonia's leader Carles Puigdemont said the region won the right to break away from Spain.
However, Spanish Prime Minister Mariano Rajoy said the plebiscite had been blocked, saying "today there has not been a self-determination referendum in Catalonia."
At least 92 people were confirmed injured out of a total of 844 who needed medical attention, Catalan authorities said, as police cracked down on a vote Spain's central government branded a "farce".
The interior ministry said 33 police required treatment as a result of the clashes,
The violence raised alarm abroad and further heightened tensions between Rajoy's government and the authorities in Catalonia in the worst political crisis in Spain in decades.
Rajoy thanked security forces for upholding the law and doing their job.
The people of Catalonia had been tricked in to taking part in the banned vote, Rajoy said on Sunday, adding that the referendum was a strategy by the regional government against legality and democratic harmony and was a "path that leads to nowhere".
He also called to meet with all Spanish political parties to discuss the country's future following the referendum.
Spanish riot police used batons and rubber bullets to storm polling stations in Catalonia Sunday, triggering clashes as thousands turned out to vote in an independence referendum banned by Madrid.
The referendum 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".
Rajoy insisted the referendum had been blocked.
"Today there has not been a self-determination referendum in Catalonia. The rule of law remains in force with all its strength," he said in a televised address after polls closed.
From early in the day, helmeted police armed with batons moved in en masse to seal off polling stations and seize ballot boxes, sparking clashes.
Videos posted on social media show police dragging voters from polling stations by their hair, throwing people down stairs and attacking Catalan firefighters who were protecting polling stations.
"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 at one Barcelona polling station.
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 if the regional government would actually do so.
'End this farce'
Even before the vote, judicial officials ordered police to seize ballot papers, detain key organisers and shut down websites promoting the referendum after Madrid and the courts deemed it unconstitutional.
Deputy Prime Minister Soraya Saenz de Santamaria called on the Catalan authorities to call off what she dismissed as a "farce".
Thousands of people had gathered outside polling stations before dawn, joining those who had spent the night camped inside to ensure they would be open on the day.
In central Barcelona, riot police charged at demonstrators who were sitting on the ground at a polling station, and fired rubber bullets, witnesses said.
'Unjustified violence'
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 police, he said, had used "batons, rubber bullets and indiscriminate force" against people demonstrating "peacefully".
"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.
"I've voted! I've voted," one man shouted.
"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.
Over-taxed, under-funded
Although Catalans are divided over independence, most want to vote on the matter in a legal and binding plebiscite.
Pro-separatist lawmakers have pushed for a referendum since September 2015 when they won a narrow majority in Catalonia'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.
This has sparked resentment which has been further exacerbated by Spain's economic woes and helped push the secessionist cause.
Rajoy's government has come under fire for limiting its response to the crisis, and several leftwing politicians called on Sunday 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.
