The former Hansa Rostock man complained of pain in his knee after Sunday's 4-0 defeat at Kaiserslautern and an examination on Tuesday showed that he has torn cruciate ligaments.
He expected to be operated on within the next week.
The news comes as a further blow to under-fire HSV coach Kurt Jara as he attempts to guide his team up the Bundesliga table after a disastrous start to the season.
"It seems as though every possible bad thing is happening at once," the Austrian boss said.
Pieckenhagen, who has not missed a single Bundesliga encounter for the Rothosen since arriving from Rostock in 2001, will be replaced by inexperienced number two Stefan Wachter.
"Both the club and the players have got full confidence in Stefan Wachter's ability," commented Jara (pictured) ahead of Saturday's vital home clash with Schalke.
