Uchida tore a thigh muscle in the 25th minute and was replaced by substitute Hoeger, who sustained a ligament injury midway through the second half and was taken off.
"The pair will be out for the coming weeks," said Schalke in a statement.
Schalke top Champions League Group B with eight points, one ahead of Arsenal with Olympiacos on six after beating Montpellier 3-1.
They are also second in the Bundesliga, seven points behind leaders Bayern Munich.
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