Both sides struggled to create any clearcut chances during the opening 45 minutes in what was a half where defences were largely on top.
The second half was largely dominated by hosting Valencia, although at times they struggled to provide support to lone striker Roberto Soldado.
Their failure to convert possession into goals was eventually punished six minutes from time. Tino Costa was adjudged to have fouled Leo inside the area and Dominguez stepped up to dispatch the resultant penalty.
Soldado and Ever Banega had chances to draw the hosts level in the closing stages, but neither could get their attempts from inside the area on target.