However, Messi, who replaced Ivan Rakitic on the hour mark, netted his first of the season in the final quarter as the Liga champions completed the comeback.
Here, Sports Mole determines how the game was won in the Spanish capital.
On target: 3
On target: 5
Was the result fair?
Overall, Barcelona did enough to deserve their three points. They were comfortably stronger in the first half but their dominance failed to yield a reward. Even after falling behind so early in the second half, they hit back almost straight away and it was effectively one-way traffic from there. Messi's winner cannot have come as too much of a surprise for Atletico boss Diego Simeone, whose side were simply second best.
Atletico Madrid's performance
With both sides taking two wins and two clean sheets into the contest, something had to give at the Vicente Calderon, but Atletico's 100% record always looked the one most under threat throughout the first period. In truth, they rode their luck to survive a few major scares, while at the other end Torres lacked the composure he once had by thrashing wide with the hosts' best and only chance.
Nevertheless, Simeone's men enjoyed an excellent start to the second half, with Torres slowly but surely growing more influential. The Spaniard was then unfortunate to have a penalty appeal turned down when his cross was blatantly handled by Javier Mascherano. Unperturbed, the Rojiblancos continued in the same vein and Tiago's superb slingshot of a through ball was expertly tucked away by the former Liverpool hitman.
However, they conceded a cheap free kick minutes later and were made to pay dear by the excellence of Neymar. Madrid struggled from there on in and it seemed a case of when, not if, they conceded again, and it came 12 minutes from the end. Few can have been surprised. It had been on the cards for a while.
In truth, there were several positives for Atletico on the night - but the most glaring of which would be the fact that there is only one more Liga game with Messi and Barcelona to contest.
With a sleep-deprived Messi dropping to the bench following the birth of his second son in recent days, all eyes were on Rafinha as he deputised for the Argentine and joined Luis Suarez and Neymar up front. Such big shoes were always going to be tough to fill and the Brazilian struggled to exert the same influence.
As a result, the goalscoring burden fell to Neymar and Suarez, with the latter missing a glorious opportunity when he poked against the crossbar, despite the goal being at his mercy. It was as close as Barcelona came to open the scoring in a half which saw Madrid frustrate their Catalan counterparts time and again.
Despite dominating the first period, the visitors emerged from the break in sluggish fashion and Madrid - who had seen a strong penalty appeal go against them - deservedly edged ahead when Tiago split the Blaugrana's defence before Torres finished with aplomb on 51 minutes.
It only served to anger Luis Enrique's men, however, as Neymar's beautiful free kick minutes later levelled up, before Enrique kicked Simeone while he was down by introducing Messi directly after. From there, Barca dominated and Suarez executed a superbly-deft flick to release the Argentine, who made no mistake with a slick outside-of-the-boot finish.
Sports Mole's man of the match
Neymar: It probably has to be Neymar, who was the visitors' best player in the first half and his exquisite free kick proved the foundation for which the comeback was built on. Messi made the game his own from the minute he came on, but it would be a mistake to forget about Neymar's contribution prior to the Argentine's arrival.
Suarez could, and certainly should, have opened the scoring in the first half but the Uruguayan tipped Thomas Vermaelen's flick-on against the crossbar.
Antonio Miguel Mateu had a poor game in truth. First, he missed Gabi's elbow on Suarez in the first half, before rejecting two stonewall penalty appeals for both sides in the second half following blatant handballs by Mascherano and Diego Godin. One to forget for the Spanish official.
Atletico Madrid: Atleti begin their Champions League campaign on Tuesday for a trip to Turkish giants Galatasaray in Group C.
Barcelona: Likewise, the Blaugrana kick off the defence of their European title on Wednesday by facing Roma in Italy.