Wolfsburg punished the visitors for their lack of potency in front of goal as Nicklas Bendtner converted from close range as he found the corner after latching on to Vieirinha's cross, despite claims of offside from Roger Schmidt's men.
However, Leverkusen hit back when Hernandez reacted to a cross into the box from Christoph Kramer to head past Benaglio from close range just before the break.
In the second half, Wolfsburg pushed forward in numbers by hitting the visitors on the break, but Andre Schurrle could not finish the move as he put his effort over the bar.
The home side regained the lead in the 77th minute as Ricardo Rodriguez saw his effort saved by Bernd Leno, but Draxler reacted in the penalty area to turn the ball into the net.
Leverkusen threatened late in the game when Bellarabi raided into the final third and struck a powerful strike at goal, only to see his effort saved by Benaglio to secure the three points for the home side.