Protests in Catalonia left 24 people injured.
Judge Pablo Llarena decided that the five posed a flight risk, after Marta Rovira became the latest leading pro-independence figure to flee overseas to escape charges. He described the case as "an attack on the constitutional state ... of unusual gravity and persistence".
That could lead to Mr Turull being imprisoned and, at a later stage, possibly banned from public office.
The judge later ruled that Turull and four others - among them the former speaker of the Catalan parliament - would be denied bail and remanded in custody.
Following the referendum, the central government in Madrid sacked the Catalan regional government, imposed direct rule and called new elections but pro-independence parties returned with a slim majority.
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".
He was due to appear in court Friday along with several other leading separatists.
Occasional clashes broke out between riot police and protesters as the large crowds pushed against police cordons, La Vanguardia reports.
Rovira ignored the summons and announced she was taking "the road to exile".
It later emerged that she had fled into exile and Spanish media reported that she was in Switzerland.
Following the order many Catalan politicians fled Spain to avoid detention by the authorities.
Among them is former Catalan leader Carles Puigdemont, who escaped to Belgium in late October and is still there.
The High Court issued arrest warrants for other six more Catalan politicians.
Mr Puigdemont indicated his resolve wasn't shaken by the charges.
"You don't want.to start governing, because if you did, you would have come here with a candidate that didn't have to see a judge tomorrow", Arrimadas said.
Speaking in Helsinki, Puigdemont said Rovira and the others charged had his "total support" and added he would not renounce his position as a deputy in Cataluña's Parliament. Arrimadas accused them of worsening the political showdown with Spain. "It is not right for a judge to do politics", Mr Puigdemont said.
The escalated legal action against the separatists follows Catalonia's independence referendum last October, which the Spanish courts declared illegal.
In December, separatist lawmakers won 47.5 percent of the votes, but that was enough for them to keep their majority of parliamentary seats, under a system of proportional representation that favors their dominance in rural areas.
Earlier, representatives of the parties standing for Spain's territorial integrity also demanded to cancel the vote.