Police stopped Calin Georgescu in traffic in the capital Bucharest and detained him for questioning on Wednesday.
Prosecutors then said they opened criminal proceedings against him for alleged offences including "incitement to actions against the constitutional order, spreading false information and false declarations" regarding electoral campaign financing and asset disclosures.
"Calin Georgescu was about to submit his new candidacy for the presidency," his team said in a post on Facebook.
"He was taken in for questioning at the General Prosecutor's Office."
The Constitutional Court made the unprecedented move to annul the presidential election just two days before a December 8 run-off.
Georgescu - who was polling in single digits and declared zero campaign spending - surprised many when he won the first round on November 24, after which allegations of electoral violations and Russian interference emerged.
Prosecutors also said he is accused of "founding or supporting fascist, racist, xenophobic or anti-Semitic organisations, as well as publicly promoting war criminals and extremist ideologies".
Thousands of protesters took to the streets of Bucharest on Saturday in a show of support for Georgescu, who has repeatedly denied any wrongdoing and argued the election was "cancelled illegally and unconstitutionally".
New dates have been set to rerun the vote with the first round scheduled for May 4.
If no candidate obtains more than 50 per cent of the ballot, a run-off would be held two weeks later on May 18.
Georgescu remains voters' top choice in opinion polls ahead of the May re-run although it remains unclear whether he will be allowed to run.
Dozens of house searches of Georgescu supporters have also been carried out across the country, the public prosecutor's office in Bucharest said.
The searches were related to campaign financing and suspected illegal right-wing extremist propaganda.
Georgescu, who has repeatedly denied any wrongdoing, said on Facebook that authorities "are looking to invent evidence to justify the theft of the elections and to do anything to block my new candidacy for the presidency".
About 100 Georgescu supporters gathered in protest outside prosecutors' headquarters in the capital Bucharest, shouting "national unity," joined by ultranationalist members of parliament.
The supporters cheered and chanted Georgescu's name when he emerged from the building.
He will now be under judicial control for 60 days, a measure which means he will be required to check in with police at regular intervals.
Romanian Prime Minister Marcel Ciolacu said on X: "The judiciary is independent & the law must be applied regardless of persons."
Georgescu has sparked controversy in the past for describing Romanian fascist and nationalist leaders from the 1930s and 1940s as national heroes.
He has also been criticised for praising Russian President Vladimir Putin in the past as "a man who loves his country" and calling Ukraine "an invented state".
Many observers attributed Georgescu's success to his TikTok account, which has 4.3 million likes and 679,000 followers.
He gained huge traction and popularity in the weeks leading up to the first election round.
His positions include supporting Romanian farmers, reducing import dependence and ramping up local energy and food production.
He also wants to establish a "sovereign" distribution model allegedly based on participatory democracy in which "Truth, Freedom and Sovereignty are the axes of values" in Romania's development.
On foreign policy, he has cast scepticism on both NATO and the European Union, to which Romania belongs.
Members of US President Donald Trump's administration have sharply criticised Romania for annulling its election.
US Vice President JD Vance said the cancellation meant Romania does not share US values.
with Reuters and DPA
