Ten suspected members of the First Capital Command gang were shot dead overnight in the suburb of Sao Bernardo do Campo, and three were killed in the Diadema suburb, said Otavio David, a state police spokesman, on Monday.
Police believe the suspected gang members were planning to attack prisons.
Seven people were arrested and heavy calibre firearms were seized.
Last month a notorious gang attacked police stations across the city and Sao Paulo state, starting a wave of violence that left nearly 200 police, prison guards, suspected criminals and jail inmates dead.
Several gang leaders are in prison and had vowed to unleash further violence.
Last month's attacks terrified Sao Paulo, prompting businesses to shut down and people to take their children out of school. Suspected gang members torched scores of buses and attacked symbols of authority across the city.