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It was the hosts who threatened first when Jordi Xumetra rose inside the six-yard box after five minutes, but he put his header just over the crossbar.
Bilbao were handed a glorious opportunity to take the lead in the 11th minute when Juanfran was adjudged to have fouled his man inside the box, handing the visitors a penalty.
Mikel San Jose stepped up for the Basque side but could not convert from 12 yards as he put the spot kick wide of the target.
They did take the lead three minutes later, however, as Aritz Aduriz found space inside the box to hit a first-time effort that deflected past the keeper and over the line.
It was almost 2-0 in the 19th minute as Iker Muniain let fly from range, sending his powerful effort just inches over the crossbar.
Bilbao's second goal came right on the stroke of half time as Ander Herrera's cross found Aduriz, who planted an accurate header into the bottom corner to double his personal tally.
Sergio Pinto threatened with a long-range effort after the break before Levante were handed a lifeline when San Jose compounded his earlier penalty woes by turning the ball into his own net.
It was the visitors who came closest to adding to their tally in the closing stages, however, with Muniain and Aduriz both forcing saves from Keilor Navas as Bilbao claimed three important points.
There was still time for a moment of drama after the final whistle as David Barral was shown a second yellow card by the referee.