The Croat has missed recent matches due to a combination of suspension and injuries but will return for the clash against Christian Streich's side
The 67-year-old also says that Thomas Muller sustained a minor knock during the 4-0 victory over Barcelona in midweek and will wait and see before deciding on the full team.
"Let's see how the guys are today. Yesterday we had a day off and today it is hot. Muller is doubtful, but Mandzukic will be in the starting XI," he told reporters.
Heycnkes went on to comment on opposite number Christian Streich whose Freiburg side are pushing for a Champions League spot, having been close to relegation when he took over in December 2011.
"I want to praise Christian Streich and his performances as a coach," he continued.
"This style of play with those limited opportunities is fantastic. Plus he is a nice colleague."
Bayern take on the Mage Solar Stadion outfit at 15:30CET.