Pedro, who has scored 10 goals in his last six starts, scrambled home Nacho Monreal's cross just before the hour to put the world champions in control as France lost Paul Pogba who was dismissed for a second yellow card in the 78th minute.
Spain, who were overtaken at the top by France last Friday following a 1-1 home draw against Finland, now have 11 points from five games and lead Les Bleus by one point with three matches left in the race to reach next year's finals in Brazil.
Spain, unbeaten in their last 50 World Cup qualifiers dating back to March 1993, restored the fans' faith in their tactics after their surprise stumble against unfancied Finland.
"This is a very important three points. It helps support the conviction we have in our ideas," Spain coach Vicente Del Bosque told Spanish television. "Everyone has doubts at times.
"When they went down to ten men in thoery it should have been easier for us, but this is when we perhaps had the most problems. The team played like men today."
France coach Dider Deschamps told a news conference: "Possession was on Spain's side but it's not a surprise. The problem is we got more chances than them but did not convert them. In the first half we defended well but were a bit shy.
"Let's not forget the team we were playing against. We put up a good fight. But it's disappointing."
Spain were caught on the break in the 15th minute as Valbuena found Christophe Jallet on the right flank, only for Benzema to fire over the bar from the left-back's pass.
