Members unanimously passed the motion, which called the banned referendum earlier this month an "expression of the democratic will of the people of Catalonia."
The motion also called on the UN and the EU to resolve the political impasse over the referendum.
Scottish nationalists have expressed solidarity with the Catalan people in a series of demonstrations and First Minister Nicola Sturgeon has backed the right of the Catalan government to hold a vote on separation.
Following the vote, she said she was "increasingly concerned by images from Catalonia," as Spanish police forced their way into many polling stations and fired rubber bullets at protesters.
However, the SNP leadership is not keen to be seen as supporting an independence bid ruled unconstitutional by Spain's government and courts.
The resolution recognised "that the decision over Catalonia's future direction is a matter for the people who live there" but said it was "concerned by any state which seeks to deny people's right to democratically express their will."
It accused Spanish police of using "disproportionate and unnecessary force against Catalan citizens" and condemned Spain's "attempts to electronically sabotage the vote."
READ ALSO: The key events since Catalonia's vote
During a debate on the motion, SNP lawmaker Sandra White said the EU would be "complicit in these attacks on the Spanish people" unless it spoke out.
Her colleague Joanna Cherry, who was in Catalonia during the vote, said she saw "repression on a scale I never expected to see in a Western European democracy".
Members paid tribute to "the patient, determined and non violent behaviour of the voters of Catalonia" and stressed the party's support for the right to self-determination.
Alyn Smith, Scottish National Party Member of the European Parliament, warned Spain it would face repercussions for its crackdown.
"There will be police investigations, judicial investigations," he told AFP.
"There will be consequences and it is right that we should add our voice to the defence of international law and fundamental personal freedoms."
Sturgeon has deferred plans for another referendum on Scottish independence.
The SNP and other pro-independence parties in 2014 lost a vote to leave the United Kingdom, polling 45 percent against 55 percent who opted to remain.
Scottish independence is not on the agenda of the three-day conference after Sturgeon formally shelved plans until Brexit negotiations advance.