The three points were only sealed in injury-time when former Chelsea midfielder Ballack volleyed home from the edge of the area for his 16th Champions League goal.
Bender had given Leverkusen the lead in the 29th minute when he drilled the ball home from an acute angle but in a pulsating game, both sides created plenty of chances with Marwin Ogunjimi especially threatening for Genk.
Leverkusen showed first as an attacking threat, with Renato Augusto heading over a cross by Gonzalo Castro before the visitors threatened through Jeroen Simaeys - who headed over from a corner when unmarked in the box.
The Bundesliga side should have taken the lead in the 14th minute when Augusto pulled the ball back to Andre Schurrle who miscued and sent the ball over from close range.
Genk were looking good on the counter-attack and Kevin De Bruyne flashed a shot wide while Leverkusen goalkeeper Bernd Leno was forced to save from Ogunjimi.
Augusto put a close-range shot wide and Sidney Sam and Schurrle both had efforts blocked before the hosts' pressure paid off in the 29th minute.
Stefan Kiessling had originally made his way into a shooting position which defender Jose Nadson got his foot to but the ball went out to Bender who drilled home from an acute angle for his first Champions League goal.
Sam's 20-metre shot then forced a save from Laszlo Koteles, although Genk continued to impress on the counter.
The match was end to end, Schurrle bending the ball just wide from the edge of the box with Koteles also called on to parry Sam's dipping goalbound shot.
However, Genk missed a golden chance to equalise just before half-time when Ogunjimi found himself in space at the far post but managed to put his header into the side-netting.
The attacking nature of the contest continued after the break, Leno forced to dive to his left to palm away as Genk enjoyed long periods of possession in the initial stages of the second half.
However, they were grateful to Koteles who saved from Schurrle with his legs after the forward had gone past a number of players on his way into the box.
Genk threatened again, substitute Elyaniv Barda making space on the edge of the box and firing a volley goalwards but straight at Leno, who gathered the ball.
The Germans were then indebted to their young keeper when he managed to get down low and parry away Ogunjimi's goalbound header.
Genk continued to search for the equaliser, Simon Rolfes getting back to make a block on the edge of the box while Khaleem Hyland then tried his luck from range which was comfortably held by Leno.
However, the final word went to Ballack, Anele Ngcongca's half clearance fell to the veteran on the edge of the box and he volleyed home, the ball taking a deflection off Ngcongca.