Officers had found the child on Wednesday wrapped in towels and stuffed in a garbage bag following a tip from a family doctor who had stopped by the mother's residence to check on the status of her pregnancy.
The doctor called police after realising the woman had given birth, but couldn't explain where the baby was.
According to prosecutors, the 24-year-old woman has given a full confession. She was previously known to authorities who had been giving her and her two small children children unspecified social help.
Although the woman has a boyfriend, he is not considered a suspect.
The killing is the latest recent case involving violence and young children in Berlin.
Last month, a 40-year-old mother was arrested after being accused of killing her baby out of a fifth floor window of an apartment building.
Another mother was recently arrested after being accused of nearly starving her young child to death.