Pizarro out of derby with Hamburg
The Peruvian international picked up a thigh muscle problem against Hanover 96 last week.
"We hoped he could make it as the injury did not look too bad (at first). But playing him would be too big a risk," coach Thomas Schaaf told reporters on Thursday.
Werder, one point off the Bundesliga relegation play-off spot, are in desperate need of a win.