The victory at Valladolid's Jose Zorrilla stadium was Barca's 16th in 17 league matches this term and restored their nine-point advantage over second-placed Atletico Madrid, who won 1-0 at home to Celta Vigo on Friday.
Barca have a La Liga record 49 points for this stage of a campaign and are 16 ahead of champions and arch rivals Real Madrid who are third ahead of their game at fourth-placed Malaga later on Saturday.
Valladolid kept a dominant Barca at bay until two minutes before halftime when Messi, who earlier shook the frame of the goal with a free kick, played Jordi Alba through on the left and Xavi turned his low cross into the net.
Messi uncharacteristically fluffed a simple chance early in the second half but the Argentine World Player of the Year doubled Barca's lead in the 59th minute with a trademark run and finish.
Xavi's clever back heel set the Argentine on his way and Messi dinked the ball between a defender's legs before firing a low shot into the far corner.
It was his 26th La Liga goal of the campaign and his 91st of 2012, extending the calendar year record he broke earlier this month when he overhauled Gerd Mueller's 40-year-old mark of 85.
Javi Guerra pulled a goal back for Valladolid in the 89th minute before Cristian Tello added a third for Barca in added time moments after coming off the bench.
The Catalan club were without coach Tito Vilanova, who had surgery on his saliva glands on Thursday and was released from hospital only hours before Saturday's game.
Assistant coach Jordi Roura has taken charge on a temporary basis until Vilanova is well enough to return. (Reporting by Iain Rogers, editing by Ken Ferris)
- Sports & Recreation
- La Liga