Another match-winning pair from the Colombian striker now sees the capital side rise to seventh in La Liga, just two points from the promised land of a top four place
A double from Radamel Falcao was enough to hand Los Colchoneros all three points on the night and reignite their hopes of Champions League football next season, despite a late Javi Martinez reply, and inflict a second successive defeat on Marcelo Bielsa's men.
The first half was a scrappy state of affairs, as neither side struggled to gain a foothold on the match. Nevertheless, it was the hosts who showed more endeavour in the early stages, spearheaded by the dangerous Arda Turan on the left wing.
After a string of forgettable snapshots, the Turk was responsible for the half's one and only goalscoring opportunity, his backheel to find Falcao in the box, but the hitman could only manage to fire the ball just wide of the target.
The contest then exploded into life after the break, once more in the favour of Diego Simeone's men, who deservedly grabbed the opening goal, albeit helped by a piece of unconvincing defending from the Basques.
The exciting Arda featured in the build-up, drilling a cross for team-mate Adrian to finish off, but despite Gorka Iraizoz's best efforts to keep the ball out, Falcao beat Mikel San Jose to the rebound to convert.
Iraizoz was again forced into action shortly after, producing a fabulous double save. Adrian surged into his opponents' box, leaving the Bilbao defence for dead, but the Basque goalkeeper did superbly well to stop the ball, and the instant follow-up from Falcao.
But his luck did not last for long, as Atleti netted a second to secure the victory. Juanfran escaped down the left flank, and the winger expertly whipped a low cross onto the head of Falcao, increasing his tally for the match in the process.
Suddenly, the visitors were presented with an impressive chance of their own, as David Lopez's cut-back on the touchline near Thibaut Courtois' goal met Markel Susaeta, but Luis Perea somehow hacked his attempt off the line.
Bilbao managed to pull one back deep in injury time, in quite spectacular fashion through Javi Martinez, who volleyed in a low cross from close range.
But it was not enough to stop Bilbao from suffering consecutive La Liga defeats, while Atleti's hopes of finishing in the top four have been suitably buoyed.