Federal Judge Sergio Moro ordered the arrest Thursday afternoon following the midnight verdict, which potentially brings to an end Lula's third bid for the presidency.
Supreme Court justices voted 6-5 to deny Lula habeas corpus while he appeals his 12-year sentence for corruption in the sprawling Petrobras scandal that has rocked Latin American politics.
They deliberated for more than 10 hours before reaching their final verdict. Chief Justice Cármen Lúcia Antunes Rocha cast the deciding vote after midnight.
Last July, Lula was convicted of corruption and money laundering, and sentenced to almost 10 years in prison. In January, an appeals court unanimously upheld the conviction and increased the sentence to 12 years.
Wednesday's ruling does not technically disqualify Lula's presidential bid. As of mid-August, the Supreme Electoral Tribunal will review candidates' eligibility forms, but it is widely expected to reject his bid under the 'clean slate' law, which disqualifies anyone who has a criminal conviction upheld by an appeals court.