Bayern had suggested previously that Goetze's days at the club were numbered, with new manager Carlo Ancelotti refusing to guarantee the midfielder a place in the first team.
"When I completed the switch from BVB to FC Bayern in 2013, it was a conscious decision and one that I do not wish to hide from today," Goetze told Dortmund's website on Thursday.
"Three years later, and now at 24 years of age, I am able to see the decision I made back then differently. I can understand the fact that many fans were unable to understand my decision.
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"Nowadays I wouldn't make the same choice again. If I am now to return to my hometown club, then I want to try to win everyone over -- especially those who do not welcome me back with open arms -- with my performances."
Goetze won three Bundesliga titles, two German Cups, and the UEFA Super Cup with Bayern but was mostly on the bench.
The former World Cup winner was included in Germany's Euro 2016 squad, but failed to have much of an impact.
"I think the transfer is a good solution for all parties. FC Bayern thanks Mario Goetze for three years wearing the Bayern shirt and wishes him all the best for the future," Bayern chairman Karl-Heinz Rummenigge said in a statement.
His return will boost the creativity in a Dortmund side that sold attacking midfielder Henrikh Mkhitaryan to Manchester United earlier this month.
(Reporting by Shravanth Vijayakumar in Bengaluru; editing by Amlan Chakraborty)
