He is the third candidate to be chosen by the main pro-independence parties since December's regional election, after the judiciary blocked the first two choices for the post: former president Carles Puigdemont and former rank-and-file independence leader Jordi Sànchez.
Jordi Sanchez, the Catalan grassroots leader and former head of the Catalan National Assembly (ANC) who is presently incarcerated on charges of sedition and rebellion, was considered to follow Puigdemont, but the Spanish Supreme Court refused to release him from prison in order to attend the parliamentary session which would invest him with the office of the presidency.
Spanish Supreme Court Judge Pablo Llarena says that Catalan separatist politicians and civil society groups have "colluded" for the past six years to execute a plan to declare Catalonia's independence, in violation of Spain's legal order.
Rovira ignored the summons and announced she was taking "the road to exile".
But they have still not been able to form a government and face growing legal pressures.
It later emerged that she had fled into exile and Spanish media reported that she was in Switzerland.
Llarena said the five detainees posed a serious flight risk and could seek to push ahead with their plans for unilateral independence if allowed to remain at liberty.
It was in anticipation of the court decision that the two main pro-independence political parties chose to rush ahead with the investiture session late Wednesday.
Although Friday's ruling dealt an immediate blow to the secessionist movement's leadership, the fresh round of detentions could further fire up the movement's supporters, who have referred to the politicians as "political prisoners". These delivered a parliamentary majority to separatist parties, but failed to earn a majority of popular support.
The four have been in pre-trial detention for months.
As a result, Catalonia remains under direct rule from Madrid, imposed after the declaration.
The court has not yet ruled on whether they will be jailed in advance of a trial, although one of the five, Marta Rovira, said on Friday she had fled Spain and gone into exile.
The High court issued worldwide arrest warrants for six more Catalan politicians.
"Exile will be a hard road, but it is the only way I have to recover my political voice".
The unity of Spain in enshrined in the country's Constitution and secession is not allowed without a reform of the top law.
Other separatist figures were already in custody or had gone into exile overseas.
A Spanish Supreme Court probe into last year's attempt to secede Catalonia from Spain wraps up Friday with the judge expected to charge 28 regional politicians and separatist leaders with offenses that may include rebellion.
Rovira, who did not specify where she was headed, is the seventh separatist to flee overseas to escape charges.Separatist parties won regional elections in December called by Madrid after they attempted to secede, retaining their absolute majority in parliament.
The semiautonomous region has been without a leader for almost five months after central authorities took control following an illegal independence declaration.