A 61st-minute goal from Imanol Agirretxe settled a match of few chances and boosted Real Sociedad's hopes of catching Basque rivals Athletic Bilbao.
Valencia, meanwhile, slipped eight points behind seventh-placed Sevilla in their quest to reach the Europa League.
Last year's fixture was a six-goal thriller which the Basques won 4-2, but this game took a while to get going.
The only real action in the opening 45 minutes came slightly before the break, when Valencia enjoyed two chances in quick succession.
The first was a shot by Sofiane Feghouli that Claudio Bravo saved and the second saw Jonas have a go following a cross into the box from Dani Parejo, but the Brazilian fired just wide of a post.
The game took a dramatic turn on the hour mark, Valencia being inches away from taking the lead but then going behind a moment later.
Parejo sent a free-kick into the box and Jonas rose to head at goal, his effort saved by Bravo and falling to Victor Ruiz, who was offside but unable to convert from a couple of yards out.
La Real attacked immediately after the resulting free-kick, Jose Angel sending a high cross from deep into the opposing area, and Agirretxe rose to head the ball into the far corner.
Antoine Griezmann should have wrapped up the points on 68 minutes when he received the ball on the left-hand side from Agirretxe as La Real broke forward.
The Frenchman was, however, unable to beat Diego Alves, the only man standing between him and the goal.
Valencia were unable to test Bravo for the remainder of the game, their best opportunity coming five minutes from the end when Jonas' shot at goal was blocked by Inigo Martinez.
The Brazilian had one final chance at the end, but could only make minimal contact with a cross from Feghouli and the ball trickled wide of goal.
The win was just what Real Sociedad needed after losing two games on the bounce, while Valencia have now taken just a point from their last three league matches.