After failing to break into the Blues' first team, a temporary move to the Bundesliga has been accepted
The 27-year-old swapped Ligue 1 side Nantes for Stamford Bridge in September 2015 but has played only 59 seconds of first-team football for the Premier League outfit.
Speaking after the Senegalese defender passed a medical on Thursday, Werder's general manager Thomas Eichin was pleased to welcome the stopper to the Bundesliga side's ranks.
"We are very glad that after the exit of Assani Lukimya [to Liaoning Whowin] we could quickly appoint a successor."
Djilobodji will immediately take to training with the German side on Thursday afternoon.