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 semi-final tie with Real Madrid, after details of the deal started appearing in the press on Monday night.
|GERMAN FOOTBALL LATEST
|2/1||Borussia Dortmund are 2/1 with William Hill to win the Champions League
"I was not surprised that a player is going to Bayern Munich," the 53-year-old coach 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 also made light of the controversy to turn in yet another impressive performance against Madrid but Low expected nothing less from the 20-year-old.
"Mario was very good [on Wednesday]," he told ZDF. "But then, Mario is very cool on the pitch; he forgets about everything else."
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 (£31.2m) buy-out clause.