Meanwhile, Atletico Madrid pulled back some ground on Barca's healthy advantage at the top of the table following a 1-0 home win over Real Betis.
Diego Costa's second-half header at the Vicente Calderon was enough to grab the points and take advantage.
At the Mestalla, Ever Banega opened the scoring with the first shot of the match after 33 minutes, but Valencia's lead lasted just five minutes as Lionel Messi fired home from the penalty spot.
The Argentinian has now scored in 12 consecutive La Liga games, but instead of his goal heralding the start of a Barca comeback, the Catalans were instead indebted to a couple of world-class late saves from Victor Valdes.
Barca still retain a nine-point gap over Atletico, with Real Madrid a further seven points back following their shock 1-0 reverse at relegation-threatened Granada on Saturday night.
Malaga's Champions League push suffered a blow as they were held to a 1-1 home draw by lowly Real Zaragoza.
The hosts fell behind to an early Helder Postiga strike and although Alarcon Isco levelled from the penalty spot 10 minutes later, Malaga were far from their best.
Zaragoza's afternoon was soured slightly by the last-minute dismissal of Jose Mari for a second yellow card.
Mallorca's bid to revive their flagging fortunes after the January transfer window were immediately undermined by a 3-0 loss at Real Sociedad.
The Islanders called new names Fernando Tissone and Alan Hutton into their starting XI, while Antonio Lopez returned on the bench, but they failed to provide any inspiration as Mallorca instead lost ground in their survival fight.
Javi Marquez's dismissal on the half-hour, following two cautions in the space of four minutes, paved the way for Sociedad to surge to victory after half-time with goals from Gonzalo Castro, Carlos Vela and Diego Irfan.
Mallorca have now won just once in 17 league games and are four points adrift of safety.
Sevilla's resurgence under Unai Emery continued as they won for their fourth consecutive home game, 2-1 over Rayo Vallecano.
Ivan Rakitic and Alvaro Negredo got the goals either side of Alejandro Dominguez's 52nd-minute penalty.