Bayern must overturn a 2-1 deficit at the Bernabeu if they are to progress to the European final on May 26.
It will be a tough ask against a Madrid side determined to win their third consecutive Champions League crown. However, the visitors have been handed a boost going into the second leg.
Both Alaba and Martinez participated in Sunday's training session, pleasing head coach Jupp Heynckes, who will most likely be without Jerome Boateng and Arjen Robben.
Robben faces a battle against the clock to be fit in time, although it is expected that the Dutch winger will line up on the bench even if he hasn't fully recovered.
Alaba and Martinez meanwhile, are thought to be possible starters as Bayern must leave nothing to chance going into the most important game of their season.