After a wretched 12 days when they were eliminated from the Champions League by Atletico Madrid, beaten in the King's Cup final by Real Madrid and suffered a shock 1-0 reverse at lowly Granada in La Liga, Barca badly needed a morale-boosting win in front of their fans at the Nou Camp.
After they had squandered a host of chances, Aritz Aduriz fired fourth-placed Bilbao ahead five minutes into the second half, prompting rumblings of discontent among the home faithful.
Pedro levelled in the 72nd minute and Messi struck the winner three minutes later when he drove the ball powerfully into the net, the Argentina forward's 26th goal of an injury-disrupted season.
With four matches left including a trip to Barca on the final day of the season, Atletico top the standings on 85 points after Friday's 2-0 win at home to Elche.
Barca are second on 81, two ahead of Real, who have a game in hand. Bilbao are a further 17 points behind Real and well placed to secure a place in Champions League qualifying for next season.
(Writing by Iain Rogers in Madrid, editing by Ed Osmond)
