Barca completed a dazzling 3-1 win in La Liga over Atletico 10 days ago but, on their return to Camp Nou, Diego Simeone's reigning Spanish champions turned in a performance recalling memories of the organisation and intensity that saw them avoid defeat over six games against the Catalan club last season.
Luis Suarez spurned a glorious chance to break the deadlock nine minutes before half-time as a fixture responsible for numerous memorable moments over recent seasons failed to fully come to life.
Despite tightening their usual grip on possession as the match progressed, Barcelona were frustrated by a staunch Atletico backline until Sergio Busquets went down under minimal contact from Juanfran when a Messi free-kick was partially cleared.
Visiting goalkeeper Jan Oblak superbly got a firm hand to the Argentinian's 85th-minute spot-kick, but he was helpless to prevent Messi from netting the rebound.
Barcelona coach Luis Enrique stuck with the 10 outfield players who beat Atletico so convincingly earlier in the month but gave goalkeeper Marc-Andre ter Stegen his now customary recall for cup action.
In the opposite dug-out, Simeone made a similar goalkeeping call, starting with Oblak, and the Slovenian was at full stretch to keep out an early curling effort from Neymar.
Messi was Atletico’s tormentor-in-chief the last time the sides met and the Barca talisman appeared in a menacing mood once more, combining with Dani Alves and Ivan Rakitic to fire over in the 12th minute.
But relentless waves of attacks did not follow on this occasion and, by the time Gerard Pique deflected a Fernando Torres effort behind in the 32nd minute, a more even contest had developed.
The first half's clearest opportunity still fell to Barcelona - Suarez lifting a shot wastefully over from close range after Rakitic had found the forward with a sublime pass on the volley. However, Pique needed a vital interception to thwart Torres and Antoine Griezmann on a 39th-minute counter-attack.
Mario Mandzukic replaced Torres at the interval and Barcelona resumed on the front foot - Jordi Alba darting in behind the Atletico defence to fire a dangerous left-wing cross into the goalmouth.
Juanfran made an important aerial challenge to deny Neymar but, as the hour approached, Barcelona again found themselves restricted to a frustrating spell of occasional half-chances.
Andres Iniesta whipped a 25-yard shot goalwards with 16 minutes remaining, handing Oblak a routine and increasingly rare save, while Suarez took a tumble under the attentions of Uruguay international colleague Diego Godin - the match officials uninterested in his claims for a foul before a booking for dissent arrived.
Eventually, Barca's pressure in the increasingly fractious closing moments told and Messi beat Oblak at the second time of asking after his initial penalty had been saved, although Atletico will retain hopes of following up their elimination of holders and rivals Real Madrid in the previous round with another famous scalp.
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