Catalonia's leader Carles Puigdemont said the region won the right to break away from Spain, with his government claiming on Monday that 90 per cent of voters backed independence in the banned referendum which was marred by clashes.
However Spanish prime minister Mariano Rajoy declared the Sunday plebiscite had been blocked, saying that "today there has not been a self-determination referendum in Catalonia", a region deeply divided over independence.
Further adding to tensions, unions and Catalan associations called a region-wide strike for Tuesday due to "the grave violation of rights and freedoms," calling on people to take to the streets in Catalonia, a major engine for Spanish growth.
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 Mr Rajoy's government and the authorities in Catalonia in the worst political crisis in Spain in decades.
Read more: Catalonia's future unclear post-referendum, but tensions with Madrid sure to remain
Mr Rajoy called the vote a process that "only served to sow division, push citizens to confrontation and the streets to revolt", but left the door potentially open to negotiations on greater autonomy for the region.
The referendum was organised under the threat of reprisals and criminal charges but thousands of Catalans stood in defiance of the central government crying "Votarem" — "We will vote".
Mr Puigdemont, who governs Catalonia, said in an address after polls closed: "With this day of hope and suffering, the citizens of Catalonia have won the right to an independent state in the form of a republic."
He added that "millions" had turned out to vote and urged the European Union to stop looking "the other way" following the police crackdown.
In a press briefing, regional government spokesman Jordi Turull said 2.02 million Catalans voted for independence, with 2.26 million people taking part.
Camped inside overnight
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 showed 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.
Read more: Defiant Catalans go to polls as Madrid tries to shut down referendum
More than 5.3 million people had been 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 soon after a "Yes" vote but it remains unclear if the regional government will actually do so.
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.
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.
The crackdown drew a sharp rebuke from Catalan leaders and others including Nicola Sturgeon, leader of the pro-independence Scottish National Party.
Earlier Mr Puigdemont said the police had used "batons, rubber bullets and indiscriminate force" against people demonstrating "peacefully".
Riot police also stormed a polling station near Girona, smashing the glass doors of the sports centre where Mr Puigdemont was due to vote and cutting a chain to force their way in.
Read more: Spanish police storm polling station in Catalonia independence vote
But the regional government said Mr Puigdemont had managed to vote anyway in nearby Cornella del Terri.
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.
But in several areas, voting was reported to be peaceful.
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.
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, health care 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.
Mr Rajoy's government has come under fire for limiting its response to the crisis, and several left wing politicians called on Sunday for him to resign.
Read more: Referendums in Catalonia and Kurdistan turn divisions intro crisis