The transfer is set to be completed after a medical and his contract with the club will be until June 30, 2020. Gotze will start training with the club next month.
The man who got Germanys World Cup winning goal in 2014 had left the club in somewhat acrimonious circumstances three years back. Fans and supporters also said they would not have the 24-year-old back in the outfit.
But Gotze has apologised for the incident saying he would not make the same choice now.
"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," Götze was quoted as saying by the Dortmund website.
"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. Nowadays I wouldn't make the same choice again!"
Gotze added his objective now is to be at his lethal best for his hometown club.
"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. My objective is to get back to playing my best football. For all of us, the club and the BVB fans," he said.
Welcoming him back to the outfit, Borussia Dortmund's chief executive officer Hans-Joachim Watzke said, "Personally, I'm absolutely delighted that Mario has chosen to come back to Borussia Dortmund. Ever since his departure in 2013, I've always hoped that he would return to the club one day."
"At this point I would expressly like to thank the chairman of the Bayern Munich board of directors, Karl-Heinz Rummenigge," said Watzke, adding: "We have negotiated three transfers with Bayern this summer. All of our negotiations have been characterised by great seriousness and mutual trust."
At the club level, the creative midfielder has enjoyed rich success. He has scored 44 goals and set up 55 in his 156 Bundesliga matches -- the majority of which (83) came in the black and yellow colours of Borussia Dortmund.
The talented dribbler has also made 43 Champions League appearances, scoring 11 and assisting 15.
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