The attack, which was captured on film, included the use of pepper spray kicking him in the head and setting a dog on him.
After receiving emergency surgery the man, identified only as André C., appeared no longer to have been in a life threatening condition. But police said in a statement that the 50-year-old died on Friday in hospital, the Tagesspiegel newspaper reported on Saturday.
The cause of death would be confirmed through an autopsy, the statement added. Two officers who used violent tactics to subdue him are being investigated for manslaughter.
A passerby filmed police attacking André C. after he was seen walking through the streets of the city's Wedding district holding two knives and carrying an axe in his waistband. The investigation into the officers was only initiated after this video was loaded onto Youtube.
The footage shows five officers surrounding the man sitting on the ground. They can be seen spraying him twice with pepper spray, hitting him on the arm with a baton, and kicking him in the back of the neck. One officer then appears to let a police dog bite him in the head.
A police car arrived and two officers jumped out of the car holding firearms. The situation escalated when the he moved to attack the officers after they called on him to drop his weapons.
"My uncle is usually a really nice guy who wouldn't do anything to anyone," 23-year-old Martin K. told Bild after the attack. "He just drinks a bit too much. His son died 10 years ago in an accident in Thailand, and his father died six weeks ago. He hasn't really got over it yet."
State criminal investigators launched a routine investigation to determine whether the police's violence was appropriate, while police unions were quick to defend the officers shortly after the incident took place. They have not released a statement following the victim's death, though.