Real Madrid beat Valencia 3-1 on aggregate following a 1-1 Wednesday and the two sides will play the first leg of their tie next Wednesday as the result of a thrilling cup game in which Malaga lived up to their status as one of the best sides in Spain this season, reports Xinhua.
Barca, who needed a goal in order to qualify after the 2-2 draw from the first leg, played their strongest side and opened the scoring after just eight minutes thanks to Pedro Rodriguez.
That goal momentarily qualified Barca but Joaquin Sanchez levelled the score just four minutes later to delight the fans in a packed La Rosaleda Stadium.
The game was a proper cup-tie with both sides exchanging attacks but it was Gerard Pique, who has just become a father after the birth of his son with pop-singer Shakira, put the visitors back in front after controlling the ball on his front and firing past Malaga keeper Carlos Kameni five minutes into the second half.
Roque Santa Cruz then hit back for Malaga after a fine flowing move started by Seba Fernandez, which saw the ball move the length and width of the pitch following a frustrated Barca attack.
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It looked as if extra time was on the cards but a lovely combination between Cesc Fabregas and Andres Iniesta saw Iniesta score Barca's third with a low shot 15 minutes later.
Leo Messi got his name on the score-sheet with 10 minutes left to kill off any chance Malaga had of a fightback. Next week Spain can prepare for another 'El Clasico'.
Meanwhile, Atletico Madrid will face Sevilla in the other semifinal after a 1-1 draw away to Betis, which gave them a 3-1 aggregate win on the back of their 2-0 triumph in the Vicente Calderon Stadium a week ago.
Diego Costa, in the side for the injured Radamel Falcao, justified his position as the first replacement for the substitute with a goal on the stroke of halftime to give his side a 3-0 aggregate lead and leave Betis needing four goals to qualify.
The home side didn't score until the last minute when Jorge Molina netted from the penalty spot but by then it was far too late.