Thiago made 26 starts last season as Bayern romped to a fifth-straight Bundesliga champion - his best return in four seasons at the Allianz Arena which have seen him struggle with numerous knee injuries.
Coach Carlo Ancelotti said: "Together with the team of doctors and the player we decided Thiago will continue his individual program at Sabener Strasse."
Bayern take on Milan on July 22, three days before they face Chelsea. They round up their tour with a game against Inter on July 27.
Ancelotti's men return to competitive football on August 5 when they meet Borussia Dortmund in the DFL Supercup.