The Partenopei star picked up a foot injury during Saturday's loss to Parma and will miss the critical Champions League clash with BVB.
The Partenopei need to avoid defeat at the Westfalenstadion to seal progress to the next round of Europe's top competition.
However, they will have to do so without the services of their talismanic playmaker, who suffered a foot injury during Saturday's shock loss to Parma.
The club's official site confirmed that Rafa Benitez's squad trained as normal on Sunday ahead of the trip to Germany, but without Hamsik, who will not be included in the squad.
Both teams go into the key Champions League clash on the back of disheartening defeats at the weekend, with Dortmund sinking to a 3-0 defeat to arch rivals Bayern Munich at home.