There were doubts that Tito Vilanova could take on the mantle left by Pep Guardiola this summer but he has proved himself in emphatic fashion with the team notching up eleven wins and a draw so far that leaves them six points clear at the top and eleven ahead of bitter rivals Real Madrid, who play Athletic Bilbao later.
Messi opened the scoring but while Francisco Montanes brought Zaragoza level, Alex Song restored the advantage before the break. Messi got his second and his 17th of the season to ensure a victory and another record with Barca's start beating those of Real Madrid in the 1968-69 and the 1991-92 seasons.
Barca had their preferred centre-half pairing of Gerard Pique and Carles Puyol available for the first time since mid-September due to injuries and Song was chosen ahead of Javier Mascherano to play the defensive midfield role with Sergio Busquets suspended.
The main surprise for Zaragoza was the decision to play Carlos Aranda in attack rather than the in-form Helder Postiga with the likely reason that he is more of a team player who drops deep than an out-and-out striker.
Injuries and suspension forced Zaragoza to field makeshift defence with Raul Goni coming in at left back and Adam Pinter in the centre, and they struggled from the start especially on the left.
Jordi Alba crossed for Messi in the first minute and though he shot just wide the Argentine did put Barca ahead after 15 minutes with Alba again the supplier.
Messi was given plenty of room in the heart of the defence to pick his spot and slotted past keeper Roberto Jimenez. MORE (AFP) CM
Barca were looking lively and passing the ball with fluidity despite the fact that a number had been away on international duty during the week, but Zaragoza drew level out of the blue.
The home side failed to clear a corner with full-back Martin Montoya only finding the edge of the area where Montanes fired the ball back in and it found the back of the net after taking a slight deflection off Puyol.
With the ease that Barca were opening up Zaragoza there was little alarm among the Catalan faithful and five minutes later it was their idol Messi who set up the second goal. He pulled the ball back from the deadball line for Song to score a rare goal.
Barca continued to dominate the game but Zaragoza looked dangerous when they did attack with Victor Rodriguez and Montanes going close with shots from distance before the break.
The home side then dropped their level with passes going astray, giving some hope to Zaragoza on the counter-attack.
But Messi responded to wrap the game up with half an hour to go with another clinical finish. This time he was found by the right full-back Montoya and he found the bottom corner from the edge of the area.
Earlier, a contentious late penalty by Roberto Soldado condemned nine-man Espanyol to a 2-1 defeat by Valencia.
Bottom-side Espanyol more than held their own after Samuele Longo equalised Jonathan Viera's opener but minutes from the end Hector Moreno was adjudged to have handled in the area. Replays suggest the ball hit his chest.
Moreno and Sergio Garcia were dismissed for complaining.
Elsewhere, Malaga drew 0-0 away to Osasuna.