Barca had conceded just one goal in eight league games this season prior to the visit to the Santiago Bernabeu, but two clinical finishes from Benzema and Valverde saw it two goals down at the interval.
Xavi's side pulled one back with seven minutes remaining through Ferran Torres, but the host restored its two-goal advantage in stoppage time courtesy of Rodrygo's penalty.
The result marked Barca's first league defeat of the campaign, with victory for Los Blancos moving them three points clear of their great rival at the top of the table.
Madrid went ahead in the 12th minute when Benzema fired home from 12 yards via a deflection from Sergi Roberto after Marc-Andre ter Stegen had raced off his line to deny Vinicius Junior.
Barca was presented with a golden opportunity to restore parity in the 25th minute, yet a stretching Robert Lewandowski somehow managed to scoop the ball over the crossbar from just a few yards out after Raphinha's cross.
Xavi's men were punished for that miss 10 minutes before the interval when Valverde whipped into Ter Stegen's bottom-right corner from 20 yards.
Benzema thought he had scored a wonderful second shortly after half-time, but his curled effort from 20 yards was ruled out for offside.
Substitute Torres reduced the deficit with a simple finish at the back post after superb work from Ansu Fati, yet Rodrygo wrapped the win up for Madrid from the spot after he had been tripped by Eric Garcia – the decision given after a VAR review.
