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 hopes of Champions League football next season, despite a late Javi Martinez reply.
The first half was a scrappy state of affairs, as both sides struggled to gain a foothold on the match. Nevertheless, it was the home side which showed more endeavor 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 with 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 favor 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 teammate Adrian to finish off. 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 opponent's box, leaving the Bilbao defense for dead, but the Basque goalkeeper did superbly well to stop the ball, and the instant followup 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, who increased his tally for the match.
Suddenly, the visiting side was presented with an impressive chance of it 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.
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