Dorlan Pabon and Ruben Perez had twice given the visitors the lead in the first-half either side of Alexis Sanchez's equaliser yesterday.
However, after David Villa had once again levelled the scores, it was unsurprisingly left to Messi to decide matters as within three minutes of coming on he fired in a wonderful free-kick and then was on hand to tap home at the end of a flowing move involving Sanchez and Andres Iniesta.
A goal kick from Jose Manuel Pinto was headed back towards the Barca goal by Jorge Molina and avoided everyone on its way through to Pabon who finished confidently into Pinto's right-hand corner.
The lead only lasted six minutes as Iniesta turned wonderfully on the left and delivered a tantalising ball into the middle which Sanchez bulleted home with his head to register his sixth league goal of the season.
Spain's all-time record goalscorer inexplicably blazed over from six yards after being teed up perfectly by Iniesta and Xavi on 23 minutes.
And five minutes later Villa passed up another great opportunity as this time Cristian Tello sped to the byline and cut the ball back only for Villa to place his side-footed effort too close to Adrian.