Karim Benzema made the breakthrough from the penalty spot in the 83rd minute before adding a second in the final exchanges, and the result has seen the reigning champions climb one point above Barcelona to the summit, with the Catalan outfit in action against Espanyol on Saturday.
Eder Militao missed out for Real Madrid due to illness, while Luka Modric and Aurelien Tchouameni were not considered for starts, having only just returned to Los Blancos following the 2022 World Cup.
Real Madrid had two chances to take the lead in the 10th minute, but Marco Asensio saw his effort kept out by Real Valladolid goalkeeper Jordi Masip, before the Spanish attacker had an effort cleared off the line by Javi Sanchez.
Los Blancos wanted a penalty for a handball on Javi Sanchez, but there was no punishment for the home side, much to the frustration of the reigning champions.
Benzema was next to come close for the visitors in the 17th minute, with the Frenchman somehow missing the target from close range after Vinicius Junior had seen his effort saved by Masip.
Real Valladolid were carrying a threat themselves, and Ivan Sanchez missed the target with a strike in the 21st minute during an open period of the contest, with Toni Kroos also firing over the crossbar down the other end.
Javi Sanchez then fired a half-volley just too high in the 28th minute of the contest before Sergio Leon tested Real Madrid goalkeeper Thibaut Courtois from a tight angle.
Masip made a smart save to deny Vinicius in the 32nd minute before Courtois did brilliantly to keep out Alvaro Aguado's effort down the other end, with the home side asking plenty of questions.
Real Madrid had the final chance of the first period in the 43rd minute, but Asensio could only fire over the crossbar after being found by Federico Valverde, with the two teams entering the interval all square.
Antonio Rudiger glanced wide of the Real Valladolid post early in the second period, before Courtois had to make two excellent stops in the 67th and 68th minute, first keeping out Aguada before producing an excellent reaction save to keep out Leon, who had placed a header towards the bottom corner.
Benzema then had a curling effort kept out by Masip, but Real Madrid were awarded a penalty in the 81st minute when Javi Sanchez was penalised for a handball inside the box.
Leon was sent off for Real Valladolid during the incident, and Benzema then stepped forward to send Carlo Ancelotti's side ahead from the spot.
Both managers made changes in the period that followed, but Benzema put the match beyond the home side in the 89th minute when he registered after smart work from Eduardo Camavinga.
Next up for Real Madrid is a clash with Cacereno in the last-32 stage of the Copa del Rey on January 3, while Real Valladolid will also be in action in the same competition against Alaves on January 4.