The 22-year-old scored Die Knappen's second of the evening to seal their progress into the last 16 of the Champions League at the expense of the Swiss side.
Poor form has seen Keller's position at Veltins-Arena come under scrutiny, but Matip hinted that the dressing room is behind their manager.
"We knew what was at stake," he told UEFA.com.
"This victory was also for our manager. It is a difficult time for him right now. We want to continue working hard and try to be more consistent with our performances."
It is the fourth time in seven seasons that Schalke have reached the knockout stages of this competition.