The club said their fans had not been respected at the stadium and their 1-0 win over Campinense on Saturday would be their last match there.
"Bahia is still open to negotiations to play at the Fonte Nova arena if the (owners) consortium values and respects fans...and treats them well," the club said in a statement announcing their return to the Pituaçu ground. "It's the fans of Esporte Club Bahia that give life to the stadium."
The Fonte Nova was rebuilt at a cost of 600 million reais (around $200 million) and hosted six matches in the 2014 World Cup and three in the Confederations Cup a year earlier.
Several of the stadiums built for Brazil's World Cup have been underused since the tournament ended and at least one has been closed because of structural problems.
(Reporting by Andrew Downie; editing by Justin Palmer)
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