Los Blancos have jumped one position into fifth and are now just three points off division leaders Sevilla despite already suffering five league defeats this term.
The defeat was just Valencia's third in the league this season, but Los Che have now only won three of their 14 top-flight matches this term, which sees them stay in 13th position.
Karim Benzema sent a powerful volley just wide of the Valencia post in the third minute as Madrid made a strong start, and the home side were ahead five minutes later.
Gareth Bale tested Neto from distance in the 15th minute as Madrid continued to dominate, but Valencia were having their moments, and Kevin Gameiro fired over the crossbar in the 28th minute during an open period.
Neto again kept out Bale 15 minutes before the end of the first half, before Benzema swept the ball over the crossbar in the 37th minute as opportunities continued to arrive in the capital.
Just the one goal separated the two teams at the break, and it was a fairly even first 45 minutes at the Bernabeu.
Valencia entered the match with the joint-best defensive record in La Liga, but had only scored 11 times in their first 13 league games of the season, which was the joint-worst attacking record.
It was not too difficult to see why they had struggled as the second period developed, with Real comfortably defending their lines and Valencia spurning the chances they did create.
Bale had another off-night and was withdrawn in the 63rd minute, and Valencia boss Marcelino made all three of his changes over the course of the next nine minutes, with Michy Batshuayi among those to enter.
Isco made his return to the side in the 80th minute, meanwhile, and Real scored their second three minutes later to wrap up all three points.
It was Lucas Vazquez on the scoresheet this time, with the Spaniard turning a clever Benzema pass into the back of the net from inside the box to cap a successful night for Madrid.
REAL MADRID (4-3-3): Courtois; Carvajal, Varane, Ramos, Reguilon; Modric (Valverde 72'), Ceballos (Isco 80'), Llorente; Lucas, Benzema, Bale (Asensio 63')
VALENCIA (4-4-2): Neto; Wass (Piccini 68'), Garay, Paulista, Gaya; Soler, Coquelin (Kondogbia 68), Parejo, Guedes; Gameiro (Batshuayi 72'), Mina