The midfielder last trained on October 14 and went under the knife a month later, after aggravating the ligament injury that caused him to miss the World Cup in Brazil.
Last week Bayern coach Pep Guardiola suggested that the player would be training with the team in a matter of weeks.
The club followed that up with a statement that said: “Getting used to the ball was what was on the [training] programme today. It is the next small step towards a comeback.”
It has been a long journey back to fitness for the 23-year-old midfielder. He originally tore his right knee ligaments in March 2014 but after aggravating the injury in May, he was forced to have surgery. He then had to go under the knife for the second time in November.
As they prepare to take on Shakhtar Donetsk in the last-16 of the Champions League, the Bundesliga champions are also awaiting the return of captain Philipp Lahm and midfielder Javi Martinez.
World Cup winner Lahm broke his ankle in November and trained with a ball for the first time on Monday afternoon.
Shakhtar travel to the Allianz Arena for the second-leg of the Champions League on March 11, with the aggregate score 0-0 and both sides keen to secure their place in the quarter-finals of European football’s premier club competition.