Hummels appeared to question the 21-year-old's move to Bayern last month, with the centre-back revealing that he was "annoyed" with Gotze's decision to leave Dortmund.
However, Gotze has denied reports of a rift with his Germany international teammate.
"I read what was said. Mats apologised to me in person. There is nothing more to add," he told reporters.
Gotze is a product of Dortmund's youth academy.