The Supreme Court judge also upheld custody orders without bail for the former regional interior minister, Joaquim Forn, and the leaders of Assemblea Nacional Catalan and Omnium Cultural, two grassroots groups that have been the main drivers of the separatist bid in Catalonia.
However, today's ruling by the supreme court judge Pablo Llarena robs Mr Puigdemont and his colleagues of at least one of their gripes against Madrid.
The exiled Catalans still face national arrest warrants in Spain, and expect to be arrested if they return there.
On Monday, a Belgian court said it would rule on December 14 whether to extradite Puigdemont whilst a court in Spain made a decision to keep the former Catalan vice-president Oriol Junqueras and three other senior Catalan politicians in jail on charges of sedition, rebellion and misuse of public funds.
Prime Minister Mariano Rajoy of Spain called the elections in the hope that voters would replace the separatists who had used their fragile majority to push through the referendum on independence that Spanish courts declared illegal.
Mr Puigdemont, who is standing for re-election to the regional parliament, would nearly certainly face arrest on his return, as the charges of rebellion and sedition against him have not been lifted.
During the last regional election in 2015 separatist parties captured 47.8 percent of the vote
The crimes are punishable in Spain with decades in prison.
Last month, Spain's central government issued the warrants for Puigdemont and four of his allies-Meritxell Serret, former agriculture minister; Antoni Comín, former health minister; Lluís Puig, former culture minister; and Clara Ponsatí, former education minister.
Catalans remain deeply split on independence, and several polls suggest pro-secession parties might struggle to win enough seats to form a new regional government.
The Spanish government called the early elections in a bid to find a democratic way out of the nation's worst crisis in almost four decades. But 53-year-old contractor Jose Luis Aguirre said the attempt to unilaterally break away from Spain "is an act that can not be allowed".
The Spanish court said Puigdemont and his cabinet members had shown a willingness to return from Belgium to Spain to take part in the election.
The ruling also coincided with the official opening on Tuesday of the campaign before the December 21 elections for a new regional Parliament in Catalonia.More news: 'House of Cards' production to resume without Kevin Spacey