The two sides meet at the Allianz Arena this evening for the opening leg, with the return fixture confirmed for next Wednesday.
Despite admitting that Real are slight favourites to progress, Makaay is adamant that the Bavarians can cause their opponents some damage.
"Barcelona and Real rate as top favourites for the trophy, but I believe Bayern are big rivals for both this season," Makaay told the club's official website.
"They have the extra motivating factor of the final at their own stadium. For the players, it's a once in a lifetime chance. I do see Madrid as slight favourites, but the current Bayern team can really hurt Real.
"It's generally better to have the second match in front of your home crowd, because that's usually when these ties are settled."
Makaay spent four years as a Bayern player up until 2007.