Although Spanish authorities had declared the vote illegal and invalid, the president of the Catalan government, Artur Mas, had pushed for the referendum.
He said that two million of the region's 5.4 million people had gone to the polls in a process where pro-independence parties and organisations worked with the regional government to set up the vote.
Spanish authorities had said that the Catalan autonomous government had not established "control mechanisms" for the balloting such as taking a prior census of voters or constituting an electoral board to oversee the cleanness of the process.
Mas had defended the symbolic vote, which has been described as a "citizen participation process" for which there are no voter rolls.
Meanwhile, Spanish Justice Minister Rafael Catala said that the referendum was a "useless and sterile drill" lacking any democratic validity, a process that only served to "exacerbate" the divisions among Catalonians.
The Spanish government said that the vote was mere "political propaganda, organised by partisan forces of independence and lacking any kind of democratic validity."
Participants - all accredited residents of Catalonia at least 16 years of age - were presented with two questions: "Do you want Catalonia to be a state? and, if they answered yes, "Do you want it to be an independent state?"
Spain's Constitutional Court had accepted an appeal last Tuesday by the central government against the vote, automatically suspending it while deliberations continued.
Spain's 1978 Constitution reserves for the national government the power to convene referendums and does not include a means for one part of Spanish territory to secede, saying that all Spaniards must decide about the future of their country.
Spanish Prime Minister Mariano Rajoy, on numerous occasions, has publicly declared his willingness to engage in dialogue with Mas, provided that it be done based on the premise of respect for the law and the Constitution.
Spain is one of the most decentralised states in the European Union in which Catalonia enjoys broad autonomy, with its own government, parliament and police.
The recent economic crisis and the refusal of authorities in Madrid to authorise a special fiscal regime for Catalonia are at the root of the independence movement in the region, which produced approximately 20 percent of Spain's GDP.
The sovereignty challenge comes after a series of scandals involving Catalonia's Democratic Convergence of Catalonia party, which has governned the autonomous community for more than 30 years. The party's historic leader, Jordi Pujol, who was president of the region from 1980-2003, and his family are under investigation for alleged tax fraud and money laundering.