In their last 16 tie with Atletico Madrid, Roger Schmidt's men bowed out in the most agonising fashion, losing 3-2 on penalties after a 1-0 defeat had levelled the tie on aggregate.
Hakan Calhanoglu and Omer Toprak both missed from the spot before Stefan Kiessling skied the last kick prior to sudden death to see Atletico through to the quarter-finals.
Leverkusen must now regroup, as they bid to return to European football's premier club competition via their league position.
Schmidt's men occupy the fourth and final qualification spot, one place and three points better off than their opponents on Saturday.
"Now we must try to sort out our heads in the next two days and regenerate," the Leverkusen coach said. "This is obviously a difficult task at the weekend, when you played here 120 minutes, and then play at Schalke.
"But we become aware of the questions and give everything."
Schalke defender Joel Matip told the club's official website: "All the teams above us won their games at the weekend and therefore took more points than us.
"Ultimately you do lots of maths, but for us the most important thing is to focus on ourselves and collect points. On Saturday we host a direct competitor, Bayer Leverkusen, so we are desperate to win and strengthen our situation."
Leverkusen are in strong form domestically, having won three matches on the spin, while Schalke have been inconsistent of late, with just one win in five in the league.
Augsburg are just a point behind them in the race for fourth spot and Markus Weinzierl's men will fancy their chances of taking all three points from a visit to second-bottom Freiburg.
At the top, Bayern Munich's next step in their seemingly inexorable charge to another title sees them host third-placed Borussia Monchengladbach, who are unbeaten in five.
Wolfsburg, in second, are 11 points behind Bayern with nine games to go and they visit mid-table Mainz.
At the opposite end of the table, rock-bottom Stuttgart host Eintracht Frankfurt and Paderborn, who have lost four in a row, welcome Hoffenheim.
Elsewhere, struggling Hamburg take on Hertha Berlin, Borussia Dortmund put their six-match unbeaten league run to the test at Hannover and Werder Bremen travel to Cologne.
For Dortmund, too, the return to league action comes on the back of UEFA Champions League disappointment, after Carlos Tevez score twice and made another to help Juventus to a 3-0 second-leg triumph on Wednesday, as the Italians completed a 5-1 aggregate triumph.
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