After receiving a request to free the 10 Catalan leaders, Supreme Court Judge Pablo Llarena decided there was a risk that Junqueras and three others would repeat their alleged offences if released.
The highly polarized parliamentary election set for December 21 is shaping up as a plebiscite between Catalans who support secession and those who favor remaining in Spain. The withdrawal of the arrest warrant would leave him without an global legal platform to pursue his independence campaign. Junqueras was unseated along with ex-president Carles Puigdemont and the rest of Puigdemont's Cabinet after regional lawmakers passed a declaration of independence that Spanish authorities deemed illegal.
He also "highlighted the danger for the impediment of their human rights" in Spain, which provoked strong condemnation when photographs were published revealing violent attacks on voters by police during the October referendum.
The move comes a day after the five former Catalonia leaders appeared in court in Belgium - the country to which they fled to avoid arrest for charges of sedition, misuse of government funds and rebellion stemming from Catalonia's big for independence from Madrid.
Puigdemont and his associates were due to appear in a Belgian court on December 14, coincidentally, when Spanish Prime Minister Mariano Rajoy is in Brussels for a meeting of European Union (EU) leaders.
Catalan separatist parties that tried to break away from Spain would lose their absolute majority in regional parliament in elections later this month, an influential opinion poll showed Monday.
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.
The poll, in which 3,000 people were interviewed, said just over 90% of those questioned were completely certain to vote in the elections while five percent will "probably" go.
Because the Belgian penal code doesn't have an equivalent for a charge of "rebellion", the Spanish court withdrew the worldwide warrants to allow for legal action against Puigdemont, as rebellion is one of the most serious crimes attributed to him.
The judge's decision follows mounting concerns among Spanish legal experts that the Belgian judiciary could in effect limit the range of crimes for which Mr. Puigdemont and the others could be put on trial if brought back to Madrid from Brussels.