The Spaniard underwent surgery on the problem seven weeks ago and has made a quick recovery to strengthen the options available to Pep Guardiola.
Martinez has not featured for Bayern since their UEFA Super Cup triumph over Chelsea in August, missing five league games and the opening two UEFA Champions League group stage matches.
Wednesday's Group D clash with Viktoria Plzen may come too quickly for the 25-year-old, but he hopes to be involved as soon.
"I enjoyed it (training)," he told the club's official website. "I am finally back on the pitch.
"Now I hope to help the team as soon as possible in games again.
"But I need a little patience and a lot of training."
In Martinez's absence, Bayern have remained unbeaten with seven wins and one draw in all competitions.
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