Bellingham was distraught when he fell to the ground clutching the back of his left thigh after 10 minutes, but the England international was seen to be walking unaided shortly afterwards.
Vinicius Junior struck soon after Bellingham's exit, curling in a sublime shot after cutting in from the left flank but Real fans grew restless as Vallecano grew in confidence with Chavarria lashing a shot over the bar just before half-time.
De Frutos equalised with a clinical finish, sweeping in a knock-down from Alvaro Garcia with a first-time shot and Thibault Courtois stopped Vallecano taking the lead when he used his feet to save from Andrei Ratiu.
Mbappe seemed set to score when he went around Augusto Batalla after the Vallecano keeper had moved out of his penalty area, but the Real striker's shot hit the bar.
Cisse was shown the red card after he caught Cebello on the left ankle, and Real went close to taking the lead again when Camavinga's header struck the post.
Real's late pressure seemed to be for nothing until Mendy caught Diaz high up, giving Mbappe the chance to strike for his 22nd goal in La Liga.
Chavarria received his second yellow card, for a push on Rodrygo, just before full-time as Real claimed their sixth straight win in La Liga while Vallecano remained just one point and a place above the relegation zone.