Goretzka was out of contract at Schalke at the end of the season and, while the club tried to keep him in Gelsenkirchen, it was always likely he would move on.
Bayern declared their desire to take the 22-year-old to Bavaria last week, the Bundesliga champions' executive board chairman Karl-Heinz Rummenigge stating they would be "crazy" if they did not consider signing a free agent Germany international.
Speaking ahead of Sunday’s game with Hannover, Heidel told reporters: "Leon Goretzka has earlier this week informed us that he would like to leave the club and join Bayern Munich.
"We noted that with regret. Karl-Heinz Rummenigge has told us that Leon has passed his medical. We are losing a very good player.
"He has signed a contract from July 1, 2018 with Bayern. We did everything possible to keep Leon."