Schweinsteiger apologised for the incident but said he did not intentionally snub Gauck as the team collected their medals following the penalty shootout defeat by Chelsea.
"It's a misunderstanding," Schweinsteiger said on Bayern's website.
"Anyone who puts themselves in my position and looks at the photo can see that, after such a great disappointment, I was not aware of what was going on around me.
"I was desperate, disappointed, as if I was paralysed. I didn't see the president's hand.
"I'm sorry that in that moment I left the wrong impression. I would like to apologise to the president."