The five, who face accusations of rebellion and sedition in Spain, are due to appear later Sunday before a judge who will decide within 24 hours whether to detain or release them.
It is the latest dramatic development in the crisis unleashed by the Catalan separatists' push for independence from Spain that sent shock waves across Europe.
Puigdemont and his allies fled to Belgium last Monday after Spain sacked the Catalan executive and imposed direct rule on Madrid following the regional parliament's declaration of independence last month.
"They were deprived of their liberty at 9.17 am (0817 GMT)," the Belgian prosecutor's office said.
"We were in regular contact with the lawyers of the five people and they agreed to turn up at the police station," prosecution spokesman Gilles Dejemeppe said. "They honoured that commitment."
Only the five, their lawyer and an interpreter will be present at Sunday's hearing.
Spain issued a warrant for their arrest on Friday after they failed to appear before a judge on claims of sedition, rebellion and misuse of public funds over the move to declare Catalonia an independent republic.
The judge in Madrid had on Thursday put Puigdemont's deputy and seven other deposed regional ministers behind bars because of a risk that they would flee.
Guarantees of fair trial
Puigdemont, 54, who insists that Catalonia earned the right to declare independence following a disputed referendum last month, had said Friday that he was willing to cooperate with Belgian authorities. But he said he was not convinced by guarantees of a fair trial back home, denouncing the "enormous pressure and political influence on judicial power in Spain".
The ousted Catalan leader, who still describes himself as "president," has also said he is willing to run as a candidate in Catalonia's December 21 snap election, which was organised after Madrid fired the region's government over the independence declaration.
"We want president Puigdemont to be the person who leads the big offensive we will carry out on the 21st at the polls," said Marta Pascal, spokeswoman for his PDeCAT party.
She said the conservative, pro-independence party was looking to put together a "big united list," a day after Puigdemont himself called for separatists to unite in the election.
During the last regional election in September 2015, Puigdemont's PDeCAT and the leftwing ERC party stood together in a "Together for Yes" coalition. With the help of the separatist, far-left CUP party, they held an absolute majority in the Catalan parliament, which has since been dissolved after it declared independence last month.
But there have been growing tensions between the two allies over strategy and it is not clear if they will stand together again.
ERC leader Oriol Junqueras has been in custody since Thursday along with other members of Puigdemont's dismissed government who did not flee to Belgium over their role in the independence drive.
Opinion polls published in several newspapers Sunday indicated that the ERC would come first in the December election, but that the independence coalition as a whole could lose its absolute majority.
Puigdemont's party, meanwhile, would come fourth, the surveys suggest.