Messi won the much-anticipated duel with Radamel Falcao on Sunday night to fire Barcelona to an impressive victory over Atletico and a nine-point advantage at the top of the Primera Division.
Falcao put Atletico ahead in the first half at the Nou Camp but, despite enjoying the better of the opening 45 minutes, Diego Simeone's side trailed at the break after a stunning goal from Adriano and a well-taken effort from Sergio Busquets.
Messi was a long way from his magical best but still ended up with two goals - his 89th and 90th of a remarkable 2012 - to quell Atletico's challenge in the second period.
It all added up to a wonderful night for Tito Vilanova's men who not only moved a further three points clear of second-placed Atletico at the summit but also took to the pitch moments after arch-rivals Real Madrid had been held to a surprise 2-2 draw by Espanyol at the Bernabeu.
Sergio Garcia had given the visitors a deserved lead on the half-hour but Madrid appeared to be heading for victory as goals form Cristiano Ronaldo and Fabio Coentrao either side of half-time put them in front.
However, after missing a host of chances to put the Catalans away, Jose Mourinho's men were punished two minutes from time as Juan Albin turned the ball past Iker Casillas from close range.
The point extends Madrid's unbeaten record at home this season to 12 games but they were left to rue a lacklustre first-half performance and a profligate one after the break.
Earlier, Ernesto Valverde's winning start as Valencia coach came to an end as striker Alejandro Dominguez's late penalty against his former club earned Rayo Vallecano victory at the Mestalla.
Valverde had guided his new side to three successive away victories - one in the Copa del Rey, one in the Primera Division and one in the Champions League - without them conceding a goal since replacing Mauricio Pellegrini earlier this month.
But that fine run - and his home debut - was ruined by Dominguez as Valencia's league woes returned.
Levante moved back up into fifth with a hard-fought 1-0 victory at Zaragoza courtesy of Ruben Garcia's first-half strike.
The visitors had fired an early warning shot when Jose Barkero smashed a shot off the post, but they eventually went in front on 19 minutes when Garcia pounced on a loose ball bouncing around the Zaragoza area to slot home only his second senior goal.
Zaragoza pushed hard for an equaliser after the break but they could not find a way through Levante's resilient defence as efforts from Paco Montanes and Edu Oriol flew just off target, whilst a late penalty claim for a handball by Juanfran was waived away by Ignacio Iglesias Villanueva.