"Peseiro was part of another page of Braga's successes over the last few years," the Portuguese Primera Liga club statement said, adding the decision was by mutual agreement.
The northern club, which has been challenging the dominance of Porto, Benfica and Sporting, finished fourth in the league this season, just failing to qualify for the Champions League.
Braga came bottom of their group in this season's Champions League with only one win at Galatasaray.
Peseiro's League Cup triumph, a shock 1-0 win over eventual league champions Porto, was the club's first trophy since 1966.
In 2012 Braga's then coach Leonardo Jardim also left the club "by mutual consent" after one season in charge having taken them to third place in the league.