Franco, a human rights and women's rights activist, was a rising star in the Socialism and Liberty Party.
Ronnie Lessa, a retired military police officer, and Élcio Vieira Queiroz, a former police officer, have been arrested, the Guardian reports. As was rumored by the investigation, both men were previously affiliated to the Military Police of Rio de Janeiro.
Law enforcement became increasingly suspicious of Mr. Lessa after realizing he was the target of a shooting, one month after the assassination of Ms. Franco, in Barra da Tijuca. Franco and Gomes were returning from a meeting Franco had attended on empowering black women when their vehicle was attacked.
Police and prosecutors detailed a "practically ideal crime" that demonstrated "knowledge of the legal and judicial system", which added to the complexity of solving the crime. Investigators said they have no reason to think that any of the Bolsonaros are linked to Franco's killing.
Prosecutors said they were able to identify Lessa as the shooter through an image of the shooter's arm, where they could see the outline of dark parts of a tattoo through a sleeve. "The case is not yet over", said one local prosecutor, who asked for anonymity to comment about a case in which he was not involved.
One suspect lives same gated community that Brazil's new far-right president Jair Bolsonaro lived in before he took office on January 1, police said.
Franco's partner Monica Benicio told AFP the arrests were "a crucial step". "We are calling for the Brazilian authorities to ensure that investigations are independent and impartial, and to bring all those responsible, including those who ordered the crime, to justice in fair trials".
Ms Franco had been highly critical of the deployment of federal security forces to Rio's poor neighbourhoods.
Police and politicians in the state have been under intense pressure to solve the killing, which included sophisticated planning by the assassins, right down to making sure surveillance cameras were shut off on the street where the attack happened.
Witzel, a former judge who was inaugurated January 1, was criticized previous year when he participated in a rally with other candidates who had broken a street sign commemorating Franco.
A close ally of Bolsonaro, Witzel ran on promises to get tough on crime in a state traditionally riddled with it, including by using sharpshooters to take out armed drug dealers in favelas. Economists say the reform is key to steadying the country's rickety public finances.