Brazilian forward Vinicius, Madrid's match-winner in Wednesday's 1-0 win over Real Valladolid, also gave his side the lead at Levante, controlling a loose ball inside the area and taking his time to curl into the far corner in the 16th minute.
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Real missed chances to extend their lead but in the end had to rely on another exceptional performance from goalkeeper Courtois to see out the victory, before Benzema added their second goal deep in added time on the break.
The win took the champions top of the standings with 10 points after four games, despite starting the season later than many of their rivals.
"It's normal for us all to be struggling a bit in the second half so early in the season, it was very hot out there and Levante are a very good team who know how to play well," said Vinicius.
"We are still lacking a bit of sharpness but after the international break I think we're going to come back much stronger."
Levante struggled to cope with Madrid for much of the first half but nearly responded to Vinicius' opener when Nikola Vukcevic headed against the bar after half an hour.
Madrid should have put the game out of Levante's reach in a blistering start to the second period in which Benzema fired against the post and Vinicius danced past two defenders only to miss the target from close range.
Captain Sergio Ramos looked to have found the all-important second goal when he headed home from a free kick but the effort was ruled out for offside following a VAR review and Madrid ended up riding their luck to cling to their advantage.
Time was almost up when Benzema skipped through on goal unchallenged and smashed high into the net to make sure of the victory.