The 23-year-old, who has since months left on his current contract, will join Bayern on a five-year contract from July 1.
Nubel has been tipped as a long-term successor to 33-year-old Manuel Neuer, who also joined Bayern from Schalke in the summer of 2011.
Nubel was named Schalke captain at the start of the season after usurping Ralf Fahrmann as the club’s first choice goalkeeper in the 2018/2019 season.
But in the wake of Nubel’s impending departure, Schalke manager David Wagner has confirmed that the former Germany u-21 goalkeeper will pass on captainship duties to Omar Mascarell.
"We have mutually agreed that Alex will step down from his role as captain," Wagner said in quotes reported on Schalke's official Twitter page.
"We looked at all the pros and cons and decided that it's better for the team if he gives up the armband. This way we avoid constant unrest.
"In the coming months, there are bigger things to think about than this. It cannot be that one player is put under the spotlight. Alex remains an important member of the group. We need to continue to completely support every player."
Jochen Schneider, Schalke's head of sport, added: "We tried everything to convince Alex to stay. Unfortunately, it didn't work out."
