The mercurial talisman of the Camp Nou led the reigning English champions a merry dance during the first half, teasing his opponents with a series of nutmegs before creating the opening goal for Ivan Rakitic that ultimately sealed a 3-1 aggregate triumph.
City - who relied heavily on goalkeeper Joe Hart to keep them in the contest - were unable to make the impression they needed to after half-time as Sergio Aguero won and missed a late penalty, just as Messi had in the first leg at the Etihad Stadium.
Under-fire manager Manuel Pellegrini must now turn his attention back towards a Premier League title defence that has unravelled to the extent that his team face a battle to seal their return to the Champions League next term.
But, while a slump that now stands at four wins across 12 outings in all competitions has often seen City punch below their considerable weight domestically, on Wednesday they ran into a sublime side who enter Sunday's El Clasico against Real Madrid with realistic designs on the top prizes at home and abroad.
Vincent Kompany's form was under the microscope before kick-off and a lapse from the City captain almost allowed Barcelona to open the scoring in the fifth minute.
Dani Alves was alert to dispossess Kompany on the edge of his own penalty area, leaving Neymar to shoot against the base of Hart's near post before the ball rolled agonisingly across the face of goal.
Hart reacted sharply to deny Messi after the Argentina superstar combined in typically slick fashion with Andres Iniesta, although City were offered encouragement in the 13th minute when Alves made a last-ditch tackle to thwart James Milner on the end of Yaya Toure's cutback.
Messi brushed a second free-kick against the top of the netting in the 27th minute having been scythed through by David Silva - the City playmaker rightly following team-mates Fernandinho and Aleksandar Kolarov into referee Gianluca Rocchi's notebook.
The opening goal arrived four minutes later at the end of clinical counter-attack, as Messi brilliantly picked out Rakitic and the midfielder - allowed ample room by the City defence - controlled on his chest before lifting a calm finish over the on-rushing Hart.
Samir Nasri was the next City player booked for a petulant kick on Neymar and the visitors' evening threatened to collapse entirely under relentless and dazzling pressure before the interval - Suarez hitting the post having raced clear of a thoroughly disheveled defence.
The game resumed in similar fashion, with Hart in regular action to deny Iniesta, Jordi Alba and Messi inside four minutes of the restart.
Barcelona's concentration levels then appeared to slacken, with Marc-Andre ter Stegen grateful for a clutch of defenders back in his goalmouth having been robbed of possession by Aguero in the right-back area.
Suarez fired into the side netting after 63 minutes, shortly before City failed to capitalise on a scramble inside the Barca area when Jesus Navas - introduced at half-time for Nasri - pulled a poor cross behind his colleagues.
Immediately Barca sprung down field and, not for the first time, Pellegrini was grateful for Hart continuing his personal duel against Messi in admirable fashion.
Hart added to his catalogue of brilliant saves by trumping Neymar in a one-on-one and deserved to see Aguero throw his team a lifeline - but the striker's 77th-minute spot-kick was comfortably saved by Ter Stegen after a combination of Javier Mascherano and Gerard Pique brought him to ground.
Suarez hit the crossbar and Hart provided more heroics to deny Messi the goal he richly deserved as the clock ticked down on a night when Barcelona's superiority was not done justice by the scoreline.
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