Any doubts about Tito Vilanova's abilities to take up where Pep Guardiola left off after four trophy-ladened seasons look to have been misplaced with Barca nine points clear of Atletico and 13 ahead of champions Real Madrid after only 16 games.
A 4-1 thrashing of Diego Simeone's pretenders on Sunday, with another double from Messi, served to underline their dominance in a league where they have swept up 46 of 48 points so far.
Third-placed Real were held to a surprise 2-2 draw by Espanyol at the Bernabeu.
"Barca are left without rivals," Catalonia-based daily Sport gloated on Monday. "The league isn't won yet... but everyone thinks it is.
"Those who thought it would be impossible to better Guardiola's era were short-sighted. Last night, Barca won two games in one. Madrid were knocked out, and Atletico brought to their knees."
Argentina forward Messi, who is favourite to collect a fourth World Player award next month, may not have been the outstanding figure against Atletico but he won his personal duel with the league's other form striker Radamel Falcao.
Adriano's spectacular equaliser for Barca was the pick of the goals at the Nou Camp, but Messi bagged two second-half goals to help cancel out Colombia striker Falcao's deft 31st minute opener.
The 26-year-old Falcao, on the wish list for a number of top European clubs, glanced a header against the post, pulled another shot just wide and grabbed his 17th goal in La Liga with a cool one-on-one finish past Victor Valdes.
Messi, however, topped that with his brace. He has scored the same as or more than 17 other sides in La Liga with 25 so far, and took his 2012 tally for club and country to 90.
"Barcelona's overall play is very important, but he opens up and finishes off many of the matches. He is different," Simeone said of his Argentine compatriot.
Atletico's title credentials may have been dented by their failures at Real and Barca, but La Liga's only remaining 100 percent home record means the Calderon could still play a part in deciding the outcome.
Just as Atletico so far have replaced their city rivals as Barca's closest pursuers, so Falcao has usurped Cristiano Ronaldo as Messi's nearest challenger in the goal-scoring charts.
With Gonzalo Higuain and Karim Benzema both out injured, Ronaldo scored one and set up a second for Fabio Coentrao against Espanyol, taking his league tally to 14, but it was not enough.
"Cristiano played a good game, but his team mates didn't," under-pressure Real coach Jose Mourinho told a news conference. "The overall attitude was good but we lacked composure and luck."
Real face another tough trip before the winter break, away at fourth-placed Malaga on Saturday, when Barca visit Valladolid.
"We aren't stupid, we know we are in a good position in the league, but we must be prudent because the league is far from over yet," Spain and Barca midfielder Xavi told reporters.
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