"Real Betis and Quique Setien have decided that the coach will not be in charge of the club next season," said a statement from the club, who finished 10th in La Liga after coming sixth last season.
"In the last two years Setien has taken Betis back into Europe, he has increased the squad's value, he has strengthened the club's academy and he has earned massive victories which will go down as some of the best in Betis' history."
Sunday's win at the Bernabeu was Betis' second successive victory away to Real Madrid, while earlier this season Setien's side beat champions Barcelona 4-3, becoming the first team in over two years to win at the Nou Camp.
Betis also beat runners-up Atletico Madrid this season and Setien earned widespread admiration for instilling an attractive and courageous style of play in his team, geared towards having a lot of possession.
Yet his side struggled for consistency and suffered embarrassing defeats to some of the lowest-ranked teams in La Liga, including a 3-0 loss at Leganes and a 4-0 thrashing away to Levante.
Betis ended the season on 50 points, three behind seventh-placed Espanyol who took the final Europa League qualification berth.
"The club would like to show its gratitude to Setien and his coaching staff for the work they have done in these last two years," added Betis' statement.
"They have contributed to the improvement of the team and the stability of the club and we wish them well in the future on a personal and professional level."
(Reporting by Richard Martin; Editing by Toby Davis)
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