The Spaniard, who last trained on Oct. 14, had to undergo further knee surgery that month after an injury setback.
"Getting used to the ball was what was on the programme today," Bayern said in a statement. "It is the next small step towards a comeback."
Bayern coach Pep Guardiola last week sounded confident the player could be back in team training in a matter of weeks but did not give a specific date for his return.
The Spain international partially tore ligaments in his right knee, the one he initially tore in March, in an injury-plagued 2014.
Thiago was out of action for two months but aggravated the injury in May during training and required surgery, forcing him to miss the World Cup before his second operation in October.
Bundesliga leaders Bayern, taking on Shakhtar Donetsk in the Champions League round of 16, are waiting for the return of several key players, including holding midfielder Javi Martinez and captain Philipp Lahm.
Lahm trained with a ball for the first time on Monday as he prepares for his own return following a broken ankle in November.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
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