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.
Liverpool midfielder Steven Gerrard, out for three weeks with a hamstring strain, came on as a late substitute and should be able to play a more prominent role in the return leg at Anfield on March 10.
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.
In a crackling atmosphere the home side dominated the early possession and were keen to get Dutch winger Arjen Robben into the action at every opportunity.
Raul squirmed clear to test Pepe Reina with a weak shot after five minutes as Liverpool were forced on to the back foot but it all soon settled down into a cautious cat and mouse encounter.
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.
Real coach Juande Ramos brought on Guti at halftime to try and open up the visitors and Torres, struggling after an ankle knock, gave way for Ryan Babel after an hour.
Robben shook off his markers and forced Reina to tip his long-range shot over in the 70th as Real steadily tightened their grip towards the end.
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.
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