Judge Sergio Moro gave da Silva 24 hours to present himself to federal police in the southern city of Curitiba.
Lula served as president between 2003 and 2011.
Da Silva was convicted previous year of helping a construction company get sweetheart contracts in exchange for the promise of a beachfront apartment. That conviction was upheld by an appeals court in January.
In Sao Paulo, Lula backer Maria Lucia Minoto Silva, a 60-year-old history teacher, was distraught after Weber cast what proved the decisive vote on the court. He is leading in all opinion polls for the presidential election, but his conviction could bar him from running.
Critics said General Eduardo Villas Boas' statements on Twitter placed undue pressure on the court and were insensitive to the military's past role in ousting democratically-elected governments in Brazil.
A former metalworker and trade union activist, he was the first left-wing leader to make it to the presidency in Brazil in almost half a century. "As if Lula were the only thief in this country". The decision could radically alter October's presidential election and affect stability in Latin America's largest nation. Over the last four years, Brazilians have experienced near weekly police operations and arrests of elite, from top politicians to businessmen like former Odebrecht CEO Marcelo Odebrecht.
Last year, Temer was twice charged with corruption but remained in office because in both cases Congress, which must vote on criminal cases involving a sitting president, made a decision to spare him prosecution.
His defenders say the charges against him and the handling of the trial process are nothing more than an elaborate plot to keep a popular left-wing candidate off the ballot.
The country's top court has voted 6-5 to deny Lula's plea and ruled he must start serving a 12-year prison sentence for graft.
The decision as to whether Lula can stand for president will rest with the Superior Electoral Court (TSE). However, under Brazilian law he can also be forced to begin serving his sentence while he appeals. Many legal observers had said that allowing da Silva to stay out of jail could have a big impact on all the other cases related to "Car Wash" and other white-collar criminals with the means to continue appealing.
Sen. Lindbergh Farias from the Workers' Party said vigils would be organized nationwide beginning on Friday.
"In Brazil's current situation, it's worth asking our institutions and the people who is really thinking about what is best for the country and future generations, and who is only anxious about their personal interests?" the general wrote in one tweet.