The game was only minutes old when it was disrupted by environmental protestors who climbed on the roof of St Jakob's Park to unfurl a banner to bemusement of spectators, including UEFA president Michel Platini, and players.
After a stoppage of almost five minutes, the Basel defence struggled to switch on with Kevin Prince-Boateng almost capitalising on a sliced clearance to score for the visitors, only to scuff his attempt and see the ball trickle past the post.
In truth, it was a close as either side came to scoring in the first half and both teams could only muster one shot on target each during the opening 45 minutes, with Basel underperforming in comparison to their win over Chelsea.
However, Schalke started to impose themselves on the game just after the interval and a neat spin and cross from Julian Draxler was cleared only to Roman Neustadter
Schalke did take advantage early in the second half when a strange corner arrived for Draxler on the bounce and with the hosts' defence slow to react, the 20-year-old fired the ball past keeper Yann Sommer.
Indeed, the Swiss side failed to work the opposition defence that had leaked seven in its previous two games, in a surprisingly underwhelming display.
It was a vital result for Schalke who top Group E with six points, but the spectacle of the game was arguably secondary to the distraction on the roof.