Barca went into the game knowing they needed an improved performance after seeing the Primera Liga slip away from them with a 1-0 defeat away to Valladolid on Saturday, while their rivals travelled to Spain after being knocked out of the FA Cup by second division Wigan Athletic. (Agencies)
Manchester City kicked off knowing they needed to score at least twice in order to have any chance of making it into the last eight, reported media.
But after a bright start, Manuel Pellegrini's side found themselves forced to defend in their half as Barca looked to put memories of their weekend defeat in Valladolid in the past.
The Catalans were unlucky not to be awarded a penalty after nine minutes when Jolean Lescott was slow to challenge Messi and made contact with the man and not the ball.
Messi was in action again after 12 minutes with a run through the heart of the City defence only for Joe Hart to come off his line to make a block, before Barca had further reasons to be unhappy with the referee after Neymar had a goal ruled out for offside, when replays showed there was no offence.
Barca settled into a rhythm with City pushed back and the visitors created their first chance through David Silva, who curled a shot over the bar, before Barca again took a grip and tested Hart three times in almost as many minutes in the closing minutes of the half.
Neymar fired just wide, before first Xavi drew a reflex save from the England international and Neymar saw a shot headed off the line after Hart had been forced to come off his line as the Brazilian found space in the penalty area.
Edz Dzeko replaced the injured Kun Aguero at the start of the second half and the Bosnian forced Victor Valdes into a stunning save six minutes after the break.
Just when it looked as if the English side could get back into the game, they quickly ran out of steam and Messi opened the score after a rapid exchange of passes at the end of the Manchester City penalty area.
The goal left City groggy Barca were happy to keep the ball and run the clock down, although the English side should also have had a late penalty after Gerard Pique brought Dzeko down and to add insult to injury Javier Zabaleta was sent off for his protests.
Vincent Kompany scored what looked as if it would be a late equalizer in the last minute, but Dani Alves was on hand in injury time to finish off a neat move from Andres Iniesta and ensure justice was both on the night and in the tie as a whole.
Barca went into the game knowing they needed an improved performance after seeing the Primera Liga slip away from them with a 1-0 defeat away to Valladolid on Saturday, while their rivals travelled to Spain after being knocked out of the FA Cup by second division Wigan Athletic.