The fight will take place in the O2 World Berlin arena, and airs live on UFC Fight Pass.
UFC Fight Night 41 is one of two international UFC events to take place on May 31. Later in the day, Chael Sonnen vs. Wanderlei Silva is expected to headline The Ultimate Fighter Brazil 3 Finale in Brazil.
Mousasi (34-4-2) made his middleweight debut in his most recent bout with Lyoto Machida. The two headlined a UFC Fight Night event in Brazil in February, with Machida winning a unanimous decision after five rounds.
Mousasi talked about the Machida fight on UFC Tonight on Wednesday, but then was goaded into all-but confirming the fight with Munoz.
Prior to the loss to Machida, Mousasi had been on a run that saw him winning six bouts, while drawing in another.
After a year on the sidelines due to injury and a bout with depression, Munoz (13-4) returned last summer with a victory over Tim Boetsch, but then had his hopes to make a run at the middleweight title sidetracked by a loss to Machida.
Now, both men coming off of losses to Machida, Mousasi and Munoz will step in the Octagon together to determine who gets back on track.
MMAWeekly.com will have further UFC Berlin bout announcements in the coming weeks.