"The coach understands that in the current climate, it was not possible for him to continue leading the team," said the Salvador-based club in a statement on their website (www.esporteclubebahia.com.br). It added that Santana left by "mutual consent".
Following Sunday's defeat, around 50 supporters invaded the club's training headquarters where the players spend the night before games. Media reports said they were persuaded to leave by the police before the players returned from the game to collect their cars.
Santana refused to give a news conference after the match, saying only: "I need to go home. I have nothing to say."
Renowned for his clipboard and broken English, Santa replaced Jorginho who quit in early April after their previous match against Vitoria ended in a 5-1 defeat. It was Santana's fourth stint at the club.
A journeyman for much of his career, his career took an unexpected twist when he was named coach of 2010 World Cup hosts South Africa, only to be fired eight months before the tournament and replaced by Carlos Alberto Parreira.
During that time, Santana became known for his failed attempts to master English which sprouted a television commercial in which he starred, in his native Brazil.
The Brazilian championship starts at the end of May, yet six of the 20 teams have already changed coaches in the state championships which open the marathon season.
Bahia and Nautico lead the way with two changes each, followed by Flamengo, Vasco da Gama, Portuguesa and Cricuma.