They made the move after a 1-0 defeat to Hertha Berlin left the club inside the bottom three of the Bundesliga having failed to win any of their last six, including an 8-0 humbling at the hands of Bayern Munich.
Zinnbaur was appointed last September as a replacement for Mirko Slomka with the side in serious relegation danger.
Six months on, they are in an equally worrying position and Zinnbauer has wished the club all the best for the future.
“Joe Zinnbauer carried out his duties here with great passion and maximum engagement from the very first day,” said Hamburg’s director of sport Dietmar Beiersdorfer in a statement on Sunday.
“He gave everything for HSV. We’ve thanked him for this. After the recent results and in view of the overall sporting situation, though, we felt we had to make a change.”
It is now hoped Knabel can have an immediate impact with time running out.
“We’re convinced this is the best option in the current situation,” added Beiersdorfer a day after Zinnbauer was informed of the club’s decision to dismiss him on Saturday.
“Peter knows the team and the situation better than anybody and he is in a position where he can act immediately.”