The Blues manager saw his side lose 3-0 to the Bundesliga club in a preseason friendly Sunday but claims referee Harm Osmers wanted the home fans to have a good time.
The Blues were beaten 3-0 in Germany, with two of the host's goals coming from the penalty spot - including one that stemmed from an alleged John Terry handball and another for Nathan Ake's challenge on Nils Petersen late in the game.
Mourinho subsequently claimed to have "learned nothing" from the match, accusing Osmers of pandering to the home supporters.
"I learned nothing from this game," the Portuguese told reporters. "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," he continued. "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 introduced at halftime.