The summer switch, which will make Gotze the most expensive German player in history, was confirmed on the eve of the first leg of Die Schwarzgelben's Champions League semifinal tie with Real Madrid, after details of the deal started appearing in the press on Monday night.
In the end, Dortmund was totally unaffected by the news, with Jurgen Klopp's men romping to a 4-1 win over Los Blancos on Wednesday, but in discussing the deal, Low confessed that he found the way in which the story broke suspicious.
"I was not surprised that a player is going to Bayern Munich," Low told Sky Sport Germany. "This is a top destination in the league, and I'm glad that Mario will remain in the Bundesliga.
"However, the timing of the announcement surprised me, and I think that it was very questionable."
Gotze, who has been capped 22 times by Die Mannschaft, is a product of Dortmund's youth academy but is now bound for Bavaria after Bayern agreed to meet his 37 million euro buy-out clause.