While his predecessor Ernesto Valverde won two La Liga titles in two years, and has the team top once again at the halfway point this season, Setien, apart from some success in Spain’s third tier in 2011, has no coaching honours to his name.
The Argentinian playmaker's withdrawal will be a major concern for Barca, particularly given this was Messi's first start of the season after just recovering from a niggling calf injury sustained at the start of August.
Barcelona continued their preparation, on the eve of their Champions League semi-finals first leg clash with Liverpool at Camp Nou.
Barca won a penalty early in the second half when Luis Suarez was fouled and Messi converted to put the league leaders in front and the Uruguayan forward made sure of the points with a simple finish from close range in the 82nd minute.
Messi scored Barcelona's second goal against SD Eibar shortly after halftime to reach a milestone in the competition after 435 league matches.
While Torres scored twice on his final appearance for Atletico Madrid, Andre Iniesta's 22-year association with Barcelona also ended with a victory with his successor, Philippe Coutinho, proving to be the difference in a 1-0 win over Real Sociedad.
The pair of own goals by Daniele De Rossi and Kostas Manolas plus some sloppy defending that allowed Gerard Pique and Luis Suarez to also score left Roma on the verge of elimination.
Bayern Munich head coach Heynckes has a full-strength team at his disposal for their Champions Leagues match against Besiktas, while Barcelona manager Valverde says he wanted to avoid meeting Chelsea in the last 16 round of the UEFA's top tournament.
The defeat leaves Zinedine Zidane's side fourth and a whopping 16 points behind runaway La Liga leaders Barcelona
Real's hopes of retaining their La Liga title fade as goals from Luis Suarez, Lionel Messi and Aleix Vidal lift Barcelona14-points clear of their bitter rivals in the standings.
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