The results are a victory for supporters of the movement to break away from Spain.
However, they once again failed to attract a majority in favour of independence: taking 47.7% of the vote and two seats down in comparison with the last election.
Surveys in recent weeks had predicted record turnout numbers.
Why is the vote important?
Puigdemont fled to Belgium after central government authorities sacked him for pushing ahead with unilateral independence for the region. "Independence has won but in a way similar to 2015 - majority of seats but not in votes".
Catalonia is a broadly left-liberal region, with much of the political class favouring mass migration and multiculturalism, and the leaders of the independence movement tended to be staunch europhiles - until the bloc's behaviour in the referendum and its aftermath called their values into question. Catalonia is now being run by direct rule from Madrid. He gave interviews, posted statements on social media and spoke to rallies through video link.
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What is more, the emergence of two competing power centres in the ANC could hamper his reform efforts before the 2019 elections. As one analyst on the eNCA television channel said after the election, the ANC of Mandela is now "completely flawed morally".
"The Spanish state has been defeated", he said, without saying whether he would return to Spain.
Spain has an independent judiciary, of course, but it's also on Mr Rajoy's watch that opposition leaders from Catalonia have been sent to prison - and could yet face 30-year jail sentences for rebellion and sedition.
"It's increasingly clear that it will be very hard for President Puigdemont to come back to Catalonia and regain the seat he won [Thursday]", said Antoni Bassas, a political commentator in Barcelona.
What does the anti-independence victor say? Lead-up polling had favored two contenders, the ERC on the pro-independence side and Citizens on the pro-union side, in a tight race for the largest share of seats. They needed 68 to keep their grip on the 135-seat Parliament.
Arrimadas has been a strong voice of opposition in parliament and one of the leading anti-independence campaigners.
The Spanish government is meeting on Friday morning to discuss the fallout. The prime minister rejected any possibility of talks with Puigdemont. The results will be bruising for Rajoy and will do nothing to heal divisions in the region, which remains deeply and evenly divided over the independence issue. But EU officials have instead backed the Spanish prime minister in the political dispute.
The European Commission said that its stance towards Catalonia remained the same despite the election result.