The decisive moment came in the 82nd minute when Benayoun headed home a beautifully delivered Fabio Aurelio free-kick.
While the free-kick and header were both textbook, questions have to be asked of the Madrid defence, who gave the little Israeli a free run and header.
The finger will also be pointed at Gabriel Heinze, who needlessly bundled over Dirk Kuyt while the ball was in the air to give the Reds the chance to whip a cross in.
Throughout the game, the home side rarely threatened the Liverpool rearguard, being limited to shots from distance, with only Dutch winger Arjen Robben providing any spark.
Madrid golden boy Raul was handed the first chance of the match, firing a shot at Pepe Reina who saved comfortably.
Liverpool's first opportunity came from a long ball by Reina which evaded everyone but Fernando Torres. The Spanish striker raced into the box and fired across Iker Casillas, who saved well.
The rest of the half saw efforts coming from distance, twice from Robben, as well as Gonzalo Higuain and Junior Marcelo, while a trademark 60-yard shot from Xabi Alonso almost caught out Casillas on the stroke of half-time.
The second half provided more of the same from the Reds, as they continued to snuff out any pressure from Madrid and looked to counter through the likes of Benayoun and Kuyt, who toiled away endlessly.
After Liverpool lost Torres with an ankle knock that he had picked up in the first half, Madrid began to play further up-field. The only chance they mustered came through Robben, who fired a vicious shot which moved through the air and was parried by Reina.
However, the final say came from the away side, as Benayoun's header gave the Reds a famous win in front of a stunned Bernabeu crowd.