The Brazilian youngster, introduced with less than a quarter of the match left, sent a deflected shot past Jordi Masip to put Los Blancos in front late on.
Out-of-form Madrid survived a major scare, as the visitors twice hit the crossbar at 0-0, and they sealed a first league win in six attempts through a late Sergio Ramos penalty.
On their best run of form in La Liga since 2003, having gone seven without defeat ahead of this trip to the capital, Valladolid spent the opening quarter of the match aiming to contain their opponents.
The youngster, effectively Los Blancos' third choice in that position, sent in a number of dangerous crosses, one of which Benzema could only head at a grateful Masip.
Valladolid, with just nine league goals to their name this term, offered more attacking intent as the match wore on as Antonito chipped a shot over the bar from a promising position and Toni Villa placed his effort wide from eight yards.
Madrid left the field to whistles from the home fans at the end of the first half after coming close to conceding 41 minutes in through Enes Unal's diving header, which ended inches wide of the post.
After probing away for the first 10 minutes of the second half to no avail, the European champions finally burst into life as Casemiro was wayward from another headed chance and Reguilon had a long-range shot pushed aside by Masip.
Valladolid, sensing a rare point - or more - in this fixture, soon hit back through efforts from Toni and Ruben Alcaraz, the latter seeing his deflected shot catch out Thibaut Courtois and hit the crossbar.
If that was not a big enough warning, Toni's shot from 25 yards hit the same part of the goal frame from the visitors' next attack in a game that was left hanging in the balance with 20 minutes to go.
Kiko Olivas got in the way of the shot, succeeding only in diverting it past his wrong-footed goalkeeper for the key breakthrough goal, which Ramos calmly added to from the spot after Benzema was tripped by Fernando Calero.
REAL MADRID (4-3-3): Courtois; Odriozola, Ramos, Nacho, Reguilon; Modric, Casemiro (Isco 56'), Kroos; Asensio (Vinicius 73'), Benzema, Bale (Vazquez 71')
REAL VALLADOLID (4-4-2): Masip; Moyano (Cop 85'), Kiko, Calero, Nacho; Antonito, Michel, Alcaraz, Villa (Verdi 69'); Suarez (Plano 76'), Unal