The former Brazil defender had been in charge at the country's most popular club for 14 games since replacing Dorival Junior, sacked for refusing to take a wage cut, in March.
Jorginho became the 11th coaching victim of the Brazilian season, which runs from February to December.
Nautico have employed three coaches, Bahia and Flamengo two each with one apiece at Vasco da Gama, Portuguesa, Santos and Criciuma.
Flamengo have failed to win any of their first four games in the Brazilian championship and are 19th in the 20-team table with two points. The championship was preceded by regional tournaments.