Sergi Guardiola latched on to a through ball late on and coolly converted his finish between the legs of Real’s ex-Chelsea goalkeeper Thibaut Courtois.
Frenchman Karim Benzema thought he had won it for Real on 82 minutes with a brilliant turn and finish.
Substitute Luka Jovic headed against the crossbar for the hosts a minute after going on as a substitute.
Real went into their second league game of the season after beating Celta Vigo 3-1 in their opener with Gareth Bale once again handed a place in the starting line-up.
The Welshman came close to leaving Madrid for China in the transfer window but the move was blocked by Real president Florentino Perez.
The former Tottenham winger struck a shot wide in the first half before narrowly heading off target in the second.
Valladolid may have collected all three points themselves, but Waldo Rubio had his thumping drive pushed away by Courtois.