The pressure was on Schalke to secure a place in the last 16 with victory over Basel, after reports claimed Keller would be sacked if his side were dumped out of Europe's premier club competition.
Schalke were beaten by Hoffenheim in the German Cup last week and sit sixth in the Bundesliga, but produced a result for Keller when he really needed it.
Basel's hopes of qualifying at Schalke's expense were dented on the half-hour as defender Ivan Ivanov was sent off for hauling Adam Szalai down as the Hungarian closed on goal.
Second-half goals from Julian Draxler and Matip ensured the Gelsenkirchen outfit secured second place behind Chelsea in Group E, leaving the Swiss champions to settle for a UEFA Europa League slot.
Defender Matip hopes the victory will ease the pressure on Keller and hopes it can be a turning point for their season.
He said: "We knew what was at stake. 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."
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