The monument - a grey concrete slab that stands around five metres high - contains a window through which viewers can watch a looped video of a "never-ending" kiss between two men.
The window was smashed by unknown assailants, police confirmed on Saturday, adding the incident was being investigated.
Günter Dworek, spokesman for the Lesbian and Gay Association (LSVD) said on Sunday the attack was revolting and outrageous, and a scandal.
He said a protest against the vandalism to draw attention to on-going discrimination would be held on Monday at the memorial.
The monument is located in the heart of the capital close to the main Holocaust monument.
Hitler outlawed homosexuality in 1936 and convicted around 50,000 people for "unnatural" behaviour deemed unbecoming of the Aryan "master race."
It is estimated that the Nazis sent between 5,000 and 15,000 gays to concentration camps along with Jews, political opponents, gypsies, Jehovah's Witnesses and others considered undesirable.
Once there, few were killed right away. Most were forced to wear a pink triangle, putting them at the bottom of the camp hierarchy, and died of hunger, disease, abuse or exhaustion. Very few survived.