Jose Peseiro has left Braga by mutual consent after just one season, the club confirmed in a statement on Wednesday.
Peseiro led the club to their first trophy since 1966 this season, overseeing a 1-0 victory against Primeira Liga champions Porto in the final of the Portuguese League Cup in April.
But Braga fell short of their aim of qualifying for the UEFA Champions League after they finished fourth in the league.
"(We) appreciate all the the work and professionalism of Jose Peseiro and his technical team for their services throughout the 2012-13 season," a statement on the club's website said.
"Following what has been a period of sustained growth and success for the club in recent years, Jose Peseiro will be part of another 'page' of success for Braga.
"(We) wish Jose Peseiro and all the technical team every success in their professional future."
Braga performed poorly in Europe this season, finishing bottom of their Champions League group after registering just one victory.