Vinícius Júnior scored his fourth goal of the season in the 86th minute, and Benzema netted his sixth two minutes later to give Madrid its third straight win in the league.
The victory means that Madrid claim the top spot with 13 points, two more than defending champion Atlético Madrid, who drew 0-0 at home against Athletic Bilbao on Saturday.
Valencia entered the weekend tied for first with Madrid and Atlético and looked set to go to the apex as they opened the scoring with a goal from Hugo Duro in the 66th minute.
Valencia had won its first two matches at Mestalla for the first time since 2014-15, when it went on to win five in a row at home. Madrid was coming off three victories in all competitions, including at Inter Milan in the Champions League on Wednesday.
Madrid coach Carlo Ancelotti was left without several players because of injuries, including Gareth Bale, Toni Kroos, and Marcelo.
In other games in the league, Mikel Oyarzabal missed a first-half penalty kick as Real Sociedad was held to a 0-0 draw against Sevilla and Leandro Cabrera scored seven minutes into injury time as Espanyol salvaged a 2-2 draw at 10-man Real Betis.
Oyarzabal had his 27th-minute penalty stopped by Sevilla goalkeeper Bono, who also came up with some key saves later in the game.
It was Sociedad's second consecutive draw after three straight victories in all competitions. Sevilla drew its last three games.
Sociedad is fourth in the standings, with Sevilla in sixth place.
Aleix Vidal put Espanyol ahead in the 16th before Betis rallied with goals by Willian José in the 41st minute and Nabil Fekir in first-half stoppage time.
The hosts played a man down from the 78th after a red card for Germán Pezzella.
Espanyol, which had conceded nine minutes into stoppage time in a loss to Atlético Madrid, is yet to win in the league this season, with three draws and two losses.