Goalkeeper Manuel Almunia produced a string of stunning saves to keep the reigning European champions at bay as they passed the Gunners into submission in a magical first half-hour that had everything except the goal Pep Guardiola's side deserved.
The north Londoners, who lost Andrey Arshavin and William Gallas to injury before half-time, looked to be on their way out of Europe and potentially on the wrong end of a humiliating beating as Barcelona finally struck twice in the opening stages of the second half.
Zlatan Ibrahimovic took advantage of Almunia's charge from goal to score seconds after the break before then grabbing a crucial second away goal with a rising drive as the Swedish striker collected Xavi's pass on the hour - his first goals in 11 games against English opposition.
Nicklas Bendtner saw Arsenal's best chance saved by Barcelona keeper Victor Valdes - but it was the introduction of substitute Theo Walcott that finally gave Arsene Wenger's team the impetus to claw their way back into a tie that looked way beyond them.
He raced clear to fire under Valdes with 21 minutes left - and Cesc Fabregas turned logic on its head, given the evidence of the previous 85 minutes, by scoring from the spot after he was brought down by Barcelona captain Carles Puyol.
Puyol was sent off and misses next week's second leg, as will Fabregas after he picked up a yellow card in the first half.
Fabregas left Wenger with another worry as he limped painfully through the closing minutes after aggravating a leg injury scoring his penalty.
Barcelona are in pole position to make their way through to the semi-finals, but they will curse taking their foot off the gas and offering Arsenal some hope when they travel to the Nou Camp for the second leg.
Former Arsenal striker Thierry Henry was warmly welcomed when he made a brief appearance as a substitute, but his impact was minimal.
