A second-half double from Radamel Falcao secured a vital three points for Atletico Madrid in the race for next season's European places.
After an uneventful first 45 minutes, the hosts took the lead four minutes into the second half as Adrian Lopez freed himself just inside the area and after his initial shot was well saved by Gorka Iraizoz, Falcao was on hand to bundle home the rebound.
The Colombian doubled Atletico's advantage with a fine diving header 20 minutes from time before Javi Martinez pulled a consolation goal back in stoppage time.
Diego Simeone had recalled Arda Turan to the starting XI and the Turkish international started brightly as he forced Iraizoz into a comfortable save with a shot from distance before curling another effort just wide.
Athletic were having to do without Fernando Llorente for the second consecutive match and again lacked a focal point as they enjoyed plenty of possession without creating a clear opportunity.
Falcao saw another long-range shot drift just wide but the half was summed up when Gabi trundled a free-kick in a very dangerous position weakly into the wall.
Atletic were far more threatening after the break however and took only four minutes to break the deadlock.
Adrian showed neat footwork to open up a sight of goal on the edge of the area and after Iraizoz had got down well to parry his effort, Falcao reacted quickest to stab the ball home from close range.
The Colombian could not get enough purchase on his header from Arda's wonderful run and cross a minute later and Koke blasted over with another decent opportunity as the hosts overran a tired looking Bilbao side.
However, Iker Muniain did waste a good opening to bring the visitors level midway through the second period as he passed up a clear shooting opportunity to try and play in Oscar de Marcos, but his pass was underhit and easily intercepted.
Iraizoz then kept the visitors in the game with a brilliant double save from Adrian and Falcao in a move almost identical to the opening goal, but two minutes later the former Porto striker's second goal did arrive as he found space to head home Juanfran's tantalising cross from the right.
Athletic should have halved the arrears with six minutes remaining as David Lopez's cross presented Markel Susaeta with virtually an open goal, but the midfielder's scuffed shot allowed Miranda to clear off the line.
The visitors did eventually get on the scoresheet deep into stoppage time as Martinez tapped in, but it was too little too late for Marcelo Bielsa's men who fell to their third consecutive defeat.
