The separatist leaders, who were axed by Prime Minister Mariano Rajoy on October 27 after the Catalan parliament declared unilateral independence, are charged with rebellion, sedition and accusations such as misappropriation of the public funds.
The Supreme Court stated on Friday that the leaders of the independence movement including separatists in the regional parliament, government and independence associations were connected in the rebellious move and needed to be tried by the same court.
Until now, the Supreme Court has only been in charge of the investigation and trial of Catalan lawmakers taking part in the secession movement.
The legal action against deposed Catalan leader Carles Puigdemont, and his 13 former ministers, was previously led by Spain's lower-level National Court.
The cases against the heads of two Catalan pro-independence associations had also been pursued at the National Court.
Judge Pablo Llarena of the Supreme Court will now be presiding over all these cases, according to the Friday statement.
Judge Llarena said all the probes related to the deposed Catalan leaders should come together, especially given the fact that the charge of "rebellion" implies the "coordinated" action of all the defendants.
He has already freed former Catalan regional parliament members, saying they were not required to go to jail as long as the investigation against them goes on. This implies, according to analysts, that the new judge might order other separatist leaders, who are currently in jail, be freed as well, pending trial.
Arrest warrants have been issued for Puigdemont and four former Catalan regional government ministers but they remained in Belgium to escape incarceration. The charges brought against Puigdemont and his former ministers are severe and could see them jailed for up to 30 years.