Federal police said two officers were injured by shrapnel of a grenade thrown by the former congressman. Both went to the hospital and were later released, the statement said.
Jefferson's lawyer Gustavo Cunha said he advised his client to surrender, but he refused.
In a video posted on social media, the congressman showed an image of federal police officers arriving at his house, and later admitted in another video that he had aimed at the police car but not at the officers.
Justice Alexandre de Moraes ordered federal police to take Jefferson, an ally of President Jair Bolsonaro, to jail after the former congressman and president of PTB political party released a tape offending justice Carmem Lucia, due to decisions she made related to the presidential elections.
Jefferson was already under investigation for the alleged involvement in producing fake news, and on Friday released statements offending justice Carmem Lucia, who had decided to transfer part of Bolsonaro's air time to presidential candidate and former President Luis Inacio Lula da Silva after the leftist complained about offenses in the adversary's political ads.
Two opposition senators, Randolfe Rodrigues and Eliziane Gama had asked the Supreme Court to punish Jefferson for offending Lucia.
Bolsonaro, who tried to distance himself from Jefferson, tweeted that he "condemns the statements against minister Carmem Lucia and armed resistance against the federal police".
Lula said the issue should now be solved by the police.
(Reporting by Rodrigo Viga Gaier and Alexandre Caverni, Writing by Tatiana Bautzer; editing by Diane Craft)
By Rodrigo Viga Gaier
