A sixth game in 17 days for Schalke ended with Klaas-Jan Huntelaar moving them onto two points from two games in Group G following an impressive 1-1 stalemate away to Chelsea.
That tiring sequence included a hard-fought 2-1 home win over Borussia Dortmund in the Revierderby on Saturday in the Bundesliga.
"We were on our last legs," said Keller. "The last weeks were very exhausting for my team.
"I cannot blame anyone from my team. They tried everything but the guys are shattered."
Julian Draxler, who returning to the side after missing the derby through suspension, blamed the dropping of points on Schalke conceding the first goal.
"The sticking point was that we didn't go ahead," said the playmaker, who recently turned 21.
"After this we conceded a silly counter-attack and afterwards it was very difficult to score against very stubborn opponents.
"We had budgeted for these three points, but we still have four matches to collect enough points."
Chelsea lead Group G on four points followed by Maribor and Schalke on two apiece and Sporting on one.
Next up for Schalke in the Champions League are back-to-back matches against the Lisbon giants.
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