The England striker, who opened his account for Real when he scored in their 1-0 Champions League win over Dynamo Kiev on Tuesday, cracked home from the edge of the area after Raul had threaded the ball through the defence in the seventh minute.
But although Real dominated for long periods at the Bernabeu they failed to press home their advantage against a Valencia side that appeared to be still traumatised by their 5-1 Champions League mauling at home by Inter Milan in midweek.
Despite Saturday's defeat, Valencia remain in second place in the table, five points behind unbeaten Barcelona who entertain Osasuna at the Nou Camp on Sunday.
Real, who had taken just a point from their last three league games, move up to seventh in the standings and are now only a point adrift of last season's champions.
Earlier on Saturday, Deportivo Coruna striker Diego Tristan earned his side a 1-1 draw away to a dominant Malaga side with a well-taken header four minutes from time, cancelling out a spectacular first-half volley by the in-form Paulo Wanchope.
Real coach Mariano Garcia Remon, deciding to keep faith with the attacking lineup that helped beated Kiev in midweek, played Owen up front alongside Ronaldo while Raul dropped back on to the left side of midfield.
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The former Liverpool player fired the ball over advancing goalkeeper Santiago Canizares with the outside of his right foot after racing on to Raul's perfectly weighted through pass.
Strike partner Ronaldo went close to extending Real's lead 20 minutes later after another excellent pass from Raul but the Brazilian's right-foot shot swerved wide of the far post.
LACKING IDEAS
With Valencia coach Claudio Ranieri leaving his talented Argentine playmaker Pablo Aimar on the bench, and influential winger Vicente injured, his team seemed bereft of ideas in attack.
It took over half an hour for the champions to threaten the Real goal, midfielder Miguel Angel Angulo heading wide after Francisco Rufete had wafted in a cross from the right.
Ranieri sent on Aimar and Italian midfielder Stefano Fiore after the break in a bid to spice up his attack and Valencia succeeded in putting Real under more pressure.
Real keeper Iker Casillas denied Valencia an equaliser just before the hour when he pulled off a superb full-length save to stop a shot from David Albelda from the edge of the area.
Garcia Remon responded by strengthening his midfield with the introduction of Santiago Solari for Owen on the hour and it was just enough to keep the improving Valencia at bay.
