Luis Suarez got Barca off to a flying start as he slotted home the opener after just 54 seconds from Messi's through ball yesterday.
However, it was Valencia who enjoyed the majority of the chances thereafter and they were left to rue Dani Parejo's missed penalty in the first half.
And Messi made sure of all three points with the final kick of the game after Diego Alves had saved his initial effort.
"We scored in the first minute and then we had problems overcoming their pressing," admitted Barca boss Luis Enrique.
"The victory is deserved because one of the important facets of the game is effectiveness in front of goal. Valencia had a penalty and fortunately Bravo was very good."
Defeat, meanwhile, leaves Valencia now four points adrift of third-placed Atletico Madrid, who beat Deportivo la Coruna 2-1 thanks to a double from Antoine Griezmann.
"We played very well in the first-half and had a lot of good chances," lamented Valencia boss Nuno Espirito Santo.
Suarez scored two wonderful individual goals as Barca all but secured their place in the Champions League semi-finals with a 3-1 win away to Paris Saint-Germain on Wednesday.
And he took less than a minute to pick up from where he left off in the French capital as Sergio Busquets fed Messi and his pass was fired low past Diego Alves by Suarez for his 12th goal in as many games.
However, Valencia went on to dominate the remainder of the opening 45 minutes and were desperately unlucky still to be behind at the break.
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