A late Robert Lewandowski penalty spared hosts Bayern who struggled until a handball by Augsburg defender Reece Oxford resulted in the winning spot kick eight minutes from time.
Bayern host Villarreal on Tuesday in their Champions League quarter-final second leg, having lost the first match 1-0 away last Wednesday.
"The first half was not good from us," admitted Bayern midfielder Goretzka. "The intensity was missing.
"We will have to improve on Tuesday - and that's what we will do. The place will be on fire. Then we will deliver a performance that is Bayern-like."
Saturday's win edged Bayern closer to a 10th straight league title, extending their lead to nine points over second-placed Borussia Dortmund who beat Stuttgart 2-0 on Friday.