The Premier League club lost 3-0 to their German opponents, with two of the home side's goals coming from the penalty spot.
Eljero Elia scored the first when captain John Terry was adjudged to have handled in the area, before Ludovic Obraniak netted the game's only goal from open play eight minutes before the break.
With a lacklustre Chelsea seemingly heading for a second-half clean sheet, Nathan Ake was then penalised for bringing down Nils Petersen a minute from time - Felix Kroos stepping up to convert the resulting penalty.
Addressing the press afterwards, Mourinho claimed to have taken nothing from the match and laid the blame solely at referee Harm Osmers' door.
"I learned nothing from this game," Mourinho said. "Our expectations are not fulfilled because when we decided to have this match here in Bremen we thought about an evolution in difficulty.
"We were expecting a fast game a competitive game but we come here and the referee thought this was a circus for Bremen fans - for them to have fun - and he killed the match.
"This game for us would have been perfect. I like the Werder Bremen team - they are fast, intense and they defend with a lot of people.
"The opponent is perfect for us to compete today but we couldn't play."
Goalkeeper Thibaut Courtois made his Chelsea debut by playing the first 45 minutes, while returning club legend Didier Drogba was introduce at half-time.
