The 72-year-old is to serve a 12-year sentence following his conviction on corruption charges last year.
Judge Sergio Moro, who oversees numerous so-called "Car Wash" cases, then ordered an arrest warrant for da Silva, giving him until 5 p.m. Friday to present himself to police in Curitiba, about 260 miles (417 kilometers) southwest of Sao Bernardo do Campo, and begin serving his 12-year sentence.
Lula, who despite the scandal leads easily in polls ahead of October presidential elections, tried to get his sentence delayed in a marathon appeal at the Supreme Court in Brasilia on Wednesday, April 4.
According to reports, the pivotal vote was cast by Justice Rosa Weber against Lula's request to avoid jail and begin serving his 12-year sentence for accepting bribes.
Thousands of his supporters surrounded the building overnight, dissuading the police from trying to arrest him.
But da Silva lost his first appeal of the conviction earlier this year, and on Thursday, a court issued an order for the former president's imprisonment, denying his petition to remain free while he continues to appeal the conviction.
When he first tried to leave the metal workers union headquarters where he was holed up to turn himself in, dozens of supporters blocked a gate where a vehicle carrying da Silva was trying to exit.
Da Silva, who Brazilians simply call "Lula", did no such thing.
Lula's ownership of the apartment had reportedly not been proven yet.
Former President Luiz Inacio Lula da Silva, leaves the metal workers union headquarters in Sao Bernardo do Campo, Brazil, Saturday, April 7.
Mauricio Santoro, a political science professor at the State University of Rio de Janeiro, said that by not complying with the order on Friday da Silva "wanted to demonstrate strength and popularity, showing that he is a political leader capable of gathering a crowd in his support".
North Korea will soon have missiles capable of reaching UK, MPs warn
They also suggested he could be "dissuaded from the use of nuclear weapons, by means of a policy of deterrence and containment". And it warned North Korea might pass on its nuclear know how to other rogue states or terror groups.
Australia, Canada, England win Commonwealth Games pool golds
The 200m freestyle champion then swam the fastest split time in the relay but ran out of steam in the final few strokes. James Guy of England took the bronze. "I'm so proud of you and everything you've achieved", Wu said.
Trump defends immigration laws at tax cut event
Each family shared their heartfelt story, including Elizabeth Lilly, who was able to watch her daughter thrive in a new sport. The latest unemployment report shows the total number of people filing for unemployment fell to its lowest level since 1973.
Lula da Silva has strongly denied any wrongdoing.
Lula's everyman style and unvarnished speeches electrified masses and eventually won him two terms as president, from 2003 to 2011, when he oversaw robust economic growth and falling inequality amid a commodities boom. If I didn't believe in the law, I wouldn't have started a political party. He would spend more than a month in jail. "Lula will not be a prisoner in 2018, he'll be president and help the people once more", said Swiecik, 31.
Operation "Car Wash" was named after the service station where agents initially investigated a minor money laundering scheme in 2014, before realizing that they'd stumbled on a gargantuan web of embezzlement and bribery at state oil company Petrobras and right through the political classes.
With Lula nearly certainly knocked out of the presidential election, the race is likely to be thrown wide open.
During his speech, Lulatold cheering supporters that Brazil's top anti-corruption judge "lied" about him being given the luxury apartment by a big construction firm as a kickback.
"I will turn myself into the authorities willingly", Lula da Silva said.
Lula accused the judiciary and Brazil's most powerful media conglomerate of assisting a right-wing coup with the ultimate aim of preventing him from competing in the race.
Officials from the Unified Workers' Central (CUT), Brazil's largest trade union federation, said they were expecting dozens of convoys to arrive, bringing in supporters from across the country.
Today, anyone convicted and losing a first appeal - which is Lula's case - has to conduct any further appeals in prison.
"Let Lula stay there for a long time and all his bunch with him".
Speaking to supporters from a memorial for his late wife, Marisa Leticia Lula da Silva, he said his arrest is politically motivated and that "history will prove" that he is not guilty.