Belgian star Thibaut Courtois made his first appearance in a Chelsea shirt as he started in goal, but he could do little as Bremen took a two-goal lead into the break.
Dutch star Eljero Elia opened the scoring from the penalty spot on 18 minutes after Blues captain John Terry was penalised for handling the ball.
Ludovic Obraniak's header then doubled the hosts' advantage just before the break as he punished some static Chelsea defending.
Half-time saw Chelsea legend Didier Drogba return to the fold - as he replaced Diego Costa - but Chelsea again made little impact after the break as Werder extended their lead with a second penalty.
Nathan Ake was harshly ruled to have conceded a foul and Felix Kroos - brother of Toni - slotted home from 12 yards.
Chelsea have two matches remaining of their pre-season, with games against Ferencvaros and Real Sociedad to come before they open their Premier League campaign at Burnley.