The Abu Dhabi company acquired 90 per cent of shares in Bahia, said a statement from the club, the most popular in Brazil's populous northeast.
The price of the deal was not disclosed. Brazilian media reports said City Football Group (CFG) had agreed to pay one billion reais ($199m), including money for debt payments, player acquisitions and infrastructure investments.
"Bahia is exceptional for its size and fan base. It will be the group's second-biggest club," after Manchester City, said Ferran Soriano, chief executive of CFG.
"The group sees Bahia and Brazilian football as the biggest growth opportunity in the world. It will be up to us and other clubs to make the league grow as it deserves," he told a press conference in Salvador, the capital of Bahia state.
The purchase is CFG's first in Brazil, the world's leading exporter of footballers. The group now has stakes in 13 clubs on four continents.
The deal, which had been in the works since September, was approved in December by 99 per cent of Bahia's members.
Founded in 1931, Bahia have won the Brazilian league twice, in 1959 and 1988.
The team, who have struggled in recent years, returned to the first division this season after being relegated in 2021.
They are currently struggling at 15th place in the league, with three points from three matches.
