Despite some resolute Arsenal defending, the Barcelona forward proved to be the difference for the La Liga leaders as he scored his first goal past Petr Cech to break the deadlock in the 71st minute.
He doubled his side’s advantage from the spot 12 minutes later after being brought down by substitute Mathieu Flamini in what was the Frenchman’s first involvement in the game.
It leaves Arsene Wenger’s side, who had some decent chances of their own, a mountain to climb in the second leg at the Nou Camp in three weeks as they look to qualify for the quarter-finals for the first time since 2010, while Barcelona stay on course to become the first side to defend the trophy in the Champions League era.
Arsenal, who made nine changes from the side that drew 0-0 with Hull in the FA Cup, started brightly and as the home crowd urged them forward Mesut Ozil picked out Aaron Ramsey just inside the penalty area, but the Welshman’s shot was blocked.
The Gunners grew in confidence and excellent tackles from Laurent Koscielny on Luis Suarez and Ramsey on Messi helped their cause.
Arsenal were disciplined in defence but were quick to counter-attack and it almost paid off when Ozil pulled the ball back for Hector Bellerin to send a shot goalwards, however, the full-back’s effort was blocked into the path of Alex Oxlade-Chamberlain, who could not generate enough power to beat Marc-Andre ter Stegen.
Barcelona showed the threat they posed just before the break as Neymar slipped the ball to Messi, who flicked the ball to Suarez, but the former Liverpool striker’s pull-back was cleared.
Seconds later, Suarez was involved again as Alexis Sanchez failed to track the run of Dani Alves, who volleyed Sergio Busquets’ pass back across goal, but the Uruguayan could only glance a header wide of the far post.
Arsenal’s tactics had nullified the visitors in the first half with Barcelona not having a single shot on target in the first half, but that soon changed after the break when Cech was forced into action to deny Neymar.