The capital club, who finished the season in ninth place in Bundesliga 2, had previously announced at the end of April that former boss Uwe Neuhaus would be leaving his post after seven years with the club.
Delighted to be given a chance
"I'm delighted to be able to work at such a great club with great surroundings," said Düwel. "As someone without a huge reputation, it's great to be given a chance like this."
Düwel, who is embarking on his first post as a head coach, was an erstwhile assistant to current Hamburger SV boss Mirko Slomka at Hannover 96, a position he held until June 2013. He was also a talent scout for English Premier League side Manchester United FC for three years.