With Barca looking like they might drop points for only the fourth time this season, the Argentina forward struck a low shot in the 77th minute at the Mestalla that spun just inside the post off the outstretched arm of goalkeeper Vicente Guaita.
Messi's league leading 27th goal lifted Barca to 71 points from 26 matches. They have now won 12 of 13 away games, drawing last month at Sporting Gijon in their only slip-up on the road.
Real Madrid can trim the gap to seven points with a win at Malaga on Thursday, when the Andalusian club's coach Manuel Pellegrini returns to the Bernabeu to face the man who replaced him at Real at the end of last season, Jose Mourinho.
Another of Pellegrini's former clubs, Villarreal, breathed life into their bid for a place in next season's Champions League earlier on Wednesday when Giuseppe Rossi struck to give them a 1-0 home win over promoted Hercules.
The Italy forward sped on to Cani's through ball in the 21st minute at the Madrigal and finished past Juan Calatayud to lift Villarreal to 50 points from 26 matches, one behind Valencia.
Juan Carlos Garrido's Villarreal side, who are still alive in the Europa League, had lost two and drawn two of their last four league matches.
Barca's Brazilian defender Adriano, who provided the assist for Messi's goal when he cut in from the left wing, said his team had been made to work hard for the three points.
"It was our most difficult away game, together with the (Real match next month), but the work is not over," he said in a television interview.
"We have to work a lot to win the championship," he added, with an eye on Barca's games at Sevilla on March 13 and at Villarreal on April 3.
