Goetze had been sidelined for almost four months after picking up an adductor muscle injury in Germany's 1-0 Euro 2016 qualifying loss to Ireland on Oct. 8.
"He completed the full one-hour session, including shots on goal and a practise game, without any problems," Bayern said in a statement.
The 23-year-old 2014 World Cup winner's return could not be better timed with Spain international Martinez sustaining a knee injury and undergoing further checks to determine the length of his absence.
Martinez, who was not included in the squad for the 2-0 win over Hoffenheim on Sunday, is the second Bayern defender to suffer a recent injury with Jerome Boateng ruled out for up to three months with an adductor muscle injury.
Fellow central defender Medhi Benatia is still working on his comeback, making Holger Badstuber the only experienced central defender in coach Pep Guardiola's squad.
Bayern are on track for a record fourth Bundesliga title -- the third under Guardiola -- after remaining eight points clear at the top following Sunday's win.
They face Italy's Juventus in the Champions League round of 16 this month and are still in the German Cup.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
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