The Israeli midfielder nodded in Fabio Aurelio's freekick from wide on the right, after a tight tactical battle between the two former European champions.
Liverpool had the best two efforts in the first half, and it was just when the Spanish champions looked to be applying the pressure towards the end when Liverpool scored.
After all the pre-match speculation over the fitness of Gerrard coach Rafael Benitez left him on the bench, and fielded a starting eleven with five Spaniards -- compared to three in Real's side.
Liverpool striker Fernando Torres, a former player of Real's city rivals Atletico, was booed every time he touched the ball, but broke clear down the right for the visitors' first chance in the 21st minute, stinging Iker Casillas' hands with a fierce shot.
Real had a goal ruled out for offside after 30 minutes but again it was Liverpool who threatened when Xabi Alonso's speculative shot from just over the halfway line forced Casillas to scuttle back and push the ball over the bar.
But a clumsy foul from Gabriel Heinze wide on the right gave Liverpool their chance and Benayoun's powerful header gave Casillas no chance, as Real's nine-mach winning streak was brought to an end.
