The centre-back was substituted late in the first half during the champions' 2-0 victory at the Allianz Arena to raise concerns that he had suffered another knee injury.
Badstuber had been sidelined since 2012 due to serious knee injuries before making his long-awaited return in July.
But Bayern revealed that the 25-year-old suffered a thigh problem on Saturday and coach Guardiola is hopeful that his latest injury is not serious.
"We will get the diagnosis tomorrow [Sunday]. But I don't think it's that serious," said the former Barcelona coach.
Franck Ribery marked his first appearance of the season with a goal after coming off the substitutes bench to seal the victory for Bayern after Mario Gotze had put them in front in the the first half.
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