The two sides knew a draw would suit them both and there were precious few moments of excitement in a painfully tedious Group G clash.
The Belgians, already through, topped the pool and Basel got the point they needed to seal second spot ahead of Hungarian side Videoton, whose meeting with Sporting Lisbon was postponed because of a waterlogged pitch.
There was little urgency from either side from the off.
Marco Streller, sporting a Phantom of the Opera mask to protect his broken nose, had scored twice in a 2-2 draw in the reverse meeting in October and the striker was the first to try his luck on Thursday night.
The 31-year-old volleyed wide early on before play was broken up by a succession of fouls and free-kicks in midfield.
Basel threatened again in the 41st minute as Fabian Schar's header from Marcelo Diaz's free-kick was tipped over by goalkeeper Laszlo Koteles.
What few openings there were were coming at the Genk end, but the Swiss side never really looked like taking advantage of them.
Fabian Frei fired wide before, in the 57th minute, Streller struck a left-footed shot from deep in the area against a post.
That was as good as it got, though, and as time wore on the two sides were happy to settle for the point that sent both through.