The final straw was Saturday's 5-0 defeat at VfB Stuttgart with four of the goals coming in a disastrous first half.
On Sunday morning, television pictures showed around 200 fans marching through the snow to the club's headquarters to protest about results.
"After five defeats in a row and the 5-0 thrashing in Stuttgart, we feel compelled to take this step," general manager Michael Preetz told a news conference.
"I'm deeply disappointment by the performance we have delivered," Skibbe said after Saturday's defeat. "The first half was the worst that I have experienced as a coach.
"It was so bad that I can't find words to describe it."
It was Skibbe's second Bundesliga firing in less than a year after he was dismissed by Eintracht Frankfurt last March. In between, he spent six months at Turkish side Eskisehirspor.
