Bono could only help Vinicius Junior's 55th-minute effort into his own net at the Ramon Sanchez Pijuan Stadium to allow the visitors to leave with a 1-0 victory.
Real, who lost to Shakhtar Donetsk in the Champions League in midweek, enjoyed the better of the first half but had to withstand a concerted fightback as Sevilla, beaten 4-0 at home by Chelsea on Wednesday, attempted to scrap their way back into the game.
Bono saved from both Benzema and Raphael Varane as the half-time whistle approached, but the sides remained locked together at the break.
Vinicius got the merest of touches to Ferland Mendy's left-wing cross and Bono could only fumble the ball into his own net.
De Jong went close to an equaliser with a 59th-minute header and substitute Nemanja Gudelj drilled a venomous free-kick inches wide with 15 minutes remaining as the home side responded.
On-loan AC Milan midfielder Suso curled an 80th-minute effort agonisingly past the upright and Courtois denied Lucas Ocampos as time ran down, but both Kroos and Benzema might have cemented victory before the final whistle.