The Globo News television channel showed live footage of federal police at the residence of the governor, who was having breakfast at the time and remains in his home in custody.
Pezao is accused of taking bribes when he was vice governor under Sergio Cabral, who is currently in prison after being sentenced to a cumulative 180 years for corruption.
The police also raided the Guanabara Palace, headquarters of Rio de Janeiro's government, searching for documents.
The Superior Court of Justice issued the arrest warrant based on the confession of Carlos Miranda, a former Cabral associate, who cooperated in exchange for a sentence reduction.
According to Miranda's testimony, Pezao would have received a monthly payment of 150,000 reais (US$40,000) as well as end-of-the-year bonuses of up to one million reais, for a total of some 25 million reais, now worth about 39 million reais (US$6.49 million) from 2007 to 2015, which authorities have been authorized to seize.
The money would have been paid by companies and intermediaries bound by contracts with the Rio de Janeiro government.
Prosecutors now also allege Pezao received money from public coffers in exchange for giving political backing to members of the criminal organization. The money he received was later laundered, prosecutors said in a statement.
Wilson Witzel was elected in October to govern the state and is set to take office January 1.