El Kun struck twice, created another for Maxi and also won a penalty, which was converted by Diego Forlan. The Argie's performance overshadowed Ronaldinho's superb strike for Barca's opener.
"We were lacking aggression in the first minutes," admitted a delighted Atletico coach Javier Aguirre afterwards, "but the wonderful effort from Aguirre, a magical goal, set us on our way.
"We had some luck, but not the referee, nor good fortune, influenced this result.
"Sergio did just what I asked from him."
Aguirre added: "The team has needed to reconcile with its fans - beyond the three points won today. Barcelona was dominating early, but we believed in our chances. We are happy, yes."
Barca coach Frank Rijkaard added: "We must digest it. It is not what we wanted, but Atletico played a great game. We must continue improving."