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A 17th-minute Pepe strike proved enough for Carlo Ancelotti's men to boast a slender half-time lead, before Jese and a Joao Miranda own goal consigned the reigning champions to a heavy first-leg defeat ahead of next week's conclusion at the Vicente Calderon.
The Portugual international opened the scoring in somewhat fortuitous circumstances, taking aim from the edge of the box before watching his effort fizz into the net via a deflection from defender Emiliano Insua.
Carlo Ancelotti's men cushioned their one-goal lead by doubling the advantage shortly before the hour mark, with youngster Jese on hand to poke Angel di Maria's teasing cross past goalkeeper Thibaut Courtois.
The Madrid giants renew hostilities again on Tuesday for the conclusion of the semi-final tie.