Per Mertesacker headed the only goal of the game midway through the first half to set up a final game decider against Barcelona in two weeks' time.
Barca beat Levski Sofia in Bulgaria to leave them two points behind Werder with only the match between the two sides at the Camp Nou to come.
Jose Mourinho's side were not at their best against a team currently second in the Bundesliga and also suffered a blow when Didier Drogba limped out of the action just before the hour mark.
It was the last thing Mourinho wanted before this weekend's crunch Premiership clash with Manchester United.
Chelsea wasted a great chance to take the lead after only ten minutes when John Obi Mikel headed over the bar from five yards out after John Terry had cushioned a header back to the young Nigerian.
Play quickly moved to the other end of the pitch in a lively start to the game and Hugo Almeida fired a shot from the edge of the area just wide.
Carlo Cudicini was forced to make the first save of the match in the 14th minute when he kept out the impressive Diego's dipping drive.
Three minutes later the Brazilian sent Almeida clear but he pulled his shot disappointingly wide under pressure from Geremi.
However, Werder scored the crucial goal in the 26th minute when terrible marking by Chelsea at a corner left Mertesacker free to head powerfully past Cudicini.
It should be have been 1-1 eight minutes later though when Tim Wiese somehow kept out Michael Ballack's close-range effort after good play by Joe Cole.
Chelsea never really had any concerted pressure after the break, although they did create several half-chances.
Just after the hour Joe Cole won the ball in midfield and found Andriy Shevchenko, but when the Ukrainian tried to square the ball to the unmarked Arjen Robben inside the penalty area, his pass was cut out.
In the 71st minute Shevchenko's free-kick beat the Werder wall, but Wiese got down well to make a vital diving save and, five minutes later, Joe Cole fired in a great left-footed effort that the goalkeeper, at full stretch, did well to keep out.
Chelsea's last chance of grabbing an equaliser came with three minutes left when Michael Essien's drive flew inches wide with Wiese beaten but Werder hung on to take a crucial three points.