The Argentine World Player of the Year, who struck either side of Alex Song's debut goal for the club, took his league tally to 17 as unbeaten Barca moved on to 34 points from 12 matches. Atletico can trim the gap back to three with a win at Granada on Sunday.
Third-placed Real Madrid, seeking a seventh win in eight games after a poor start to their title defence, can close to within two points of their city rivals with a win at home to Athletic Bilbao later on Saturday.
After sending an early shot narrowly wide, Messi opened the scoring in the 16th minute at the Nou Camp when he picked up Jordi Alba's pass and clipped the ball into the bottom corner. Zaragoza pulled a goal back eight minutes later when a Francisco Montanes shot took a slight deflection of Carles Puyol, back in central defence after injury, and flew past Victor Valdes.
Song, who joined from Arsenal in the close season, thumped a Messi pullback through a crowd of players into the net to restore Barca's lead in the 28th minute and Messi curled in his second to kill off the game on the hour. It was his 78th goal of 2012 for club and country - 66 for Barca and 12 for Argentina - and he is closing in on the record for a calendar year of 85 set by German Gerd Mueller in 1972.
(Reporting by Iain Rogers, editing by Mark Meadows)