The pair both took part in team training on Sunday in Munich.
Alaba is fit again after missing Wednesday’s 2-1 defeat in the Munich first leg with a thigh injury.
Defensive midfielder Martinez has recovered after coming off with a head injury in the second half against Real.
Alaba says he is “well on the way” and is expected to resume at left-back from Rafinha, whose mistake led to Marco Asensio’s winning goal in the first leg.
“You can see in the training sessions how focused and concentrated we are working,” said Alaba.
“The mood in the team is very, very good.
“In the dressing rooms, you can see how much we want it and we’ll put in 100 percent of what we have.”
Bayern’s star forwards Thomas Mueller, Robert Lewandowski, Franck Ribery and James Rodriguez, who were all rested for Saturday’s 4-1 league win against Eintracht Frankfurt, were also put through their paces.
The German giants are waiting to see if winger Arjen Robben will recover in time from a groin strain.
Alongside long-term injury victims Manuel Neuer, Kingsley Coman and Arturo Vidal, Bayern will be without Jerome Boateng, who damaged his groin against Real.
Club chairman Karl-Heinz Rummenigge says the Bavarians will need their “best performance of the season” to win in Madrid and reach the May 26 Champions League final in Kiev.
“We are looking forward to the second leg, against the best team in the world which has won the Champions League three times since 2014,” said Rummenigge.
“Real are undoubtedly the benchmark in world football.
“If we want to realise our Kiev dream at the Bernabeu, we definitely need the best performance of the entire season.”
Tuesday is a national public holiday in Germany, however Rummenigge says it will be anything but for Bayern in Madrid.
“It will be guaranteed a day of work, and then hopefully a May public holiday,” he added.
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