In a tense session of the regional parliament, members approved the proposal to set up a seven-member "control commission", a type of electoral authority, by 86 votes with 48 abstentions.
Leaders in Catalonia are defying Madrid by pushing for a non-binding "consultation" vote on November 9th to ask Catalans whether the economically powerful northeastern region should break away from the rest of Spain.
In response to an appeal by Spain's conservative government, the country's Constitutional Court on Monday suspended the legal measures launched by the region's president, Artur Mas, in his bid to hold the vote.
The Catalan government cautiously suspended its official campaign for the poll, but thousands rallied in the streets on Tuesday vowing to push ahead with the referendum.
Enric Millo, a regional deputy for Spain's governing Popular Party (PP) warned pro-independence leaders their vote on forming a commission could have "legal consequences".
"The Catalan parliament cannot vote on this matter because that would breach and therefore disobey a ruling by the Constitutional Court," he said in Wednesday's session.
The parliamentary spokesman for Mas's CiU coalition, Jordi Trull, responded: "We can make this agreement and we will not be committing any irregularity or anything illegal."
The motion to form the voting commission has to be signed by Mas to enter into force.
Mas has promised to act legally and on Wednesday warned Catalans against the acts of "civil disobedience" that some separatist leaders have called for.
"Disobedience does not always lead to victory," he told the parliament on Wednesday.
But in the face of calls from regional representatives of Spain's ruling Popular Party to call of the vote, Mas was defiant.
"I will move away from our determination to allow the Catalan people to decide their future," he said.
The constitutional standoff has set the stage for a tense and uncertain few weeks as the long-simmering dispute over independence comes to a head.
Thousands of separatists, rallied by powerful civil pro-independence groups such as the Catalan National Assembly, massed in the rain in front of town halls across Catalonia on Tuesday, yelling: "We will vote!"
"The streets were full of people demanding we go ahead," said Gemma Calvet, a member of the left-wing pro-independence party ERC which props up Mas's coalition in the parliament.