Aritz Aduriz's brace swung the game in Bilbao's favour, but only after Mikel San Jose had missed a penalty, and they endured a nervy finish after San Jose further blotted his copybook with a 67th-minute own goal.
But the win was enough to move Bilbao six points clear of fifth-placed Sevilla, with the destiny of the Champions League qualifying place very much in their hands.
San Jose was presented with the chance to put Bilbao ahead early on after Juanfran fouled Iker Muniain in the penalty area, but his drilled spot-kick flew wide of the right-hand post.
Even so, they needed only a few more minutes to take the lead, with Aduriz finding the net in the 15th minute when he fired home from Markel Susaeta's assist.
Levante were struggling to gain a foothold in the match, not helped by Victor Casadesus mis-hitting his shot in a rare chance in front of goal, and it was Bilbao who dominated as they created further openings for Muniain, Oscar De Marcos and Erik Moran.
Although those were spurned, Aduriz made sure they could enjoy half-time in a little more comfort as he turned in Ander Herrera's cross in the 44th minute.
Levante began to improve after the break, threatening through Sergio Pinto and David Barral, but it was Bilbao's San Jose who eventually gave them the breakthrough, inadvertently turning Ruben Garcia's cross into his own net.
That woke Bilbao up, but Moran's shot was easily held by Keylor Navas, who then turned Muniain's header around the post in the 75th minute.
However, they had done enough to take three vital points, with Levante unable to muster an equaliser.