A Michael Essien strike midway through the first half and a 68th-minute Michael Ballack penalty secured maximum points, although it could have been very different had Bremen hitman Miroslav Klose been at his best.
Jose Mourinho handed a first start to Ashley Cole and also brought in Claude Makelele, with Wayne Bridge and Shaun Wright-Phillips the men to miss out. Joe Cole was named on the bench after recovering from the knee injury he suffered in pre-season.
Werder coach Thomas Schaaf recalled Germany internationals Torsten Frings and Tim Borowski, after resting them for last weekend's embarrassing cup defeat against third division side FK Pirmasens, while Klose played after passing a fitness test.
Chelsea started well and looked to exploit the pace of Andriy Shevchenko and Didier Drogba by knocking long balls over the top of a Werder backline that often strayed dangerously high.
Essien was at the centre of all Chelsea's early attacking play and it was fitting that the midfielder opened the scoring in the 24th minute - although he needed the help of Werder defender Petri Pasanen.
Frank Lampard attempted to waltz through the visiting defence only to lose possession on the edge of the box, but Pasanen inexplicably knocked the ball into Essien's path and the Ghanaian World Cup star coolly slotted the ball home.
The Blues continued to enjoy plenty of possession, but the Bundesliga side were dangerous on the break and Pierre Wome and Klose both wasted decent chances to level before the interval.
The visitors took control after half-time and Klose twice went close, heading just over and then against the bar from right-wing crosses by the hard-working Frings.
Blues skipper John Terry was uncharacteristically rattled and picked up a yellow card for a body check on Ivan Klasnic, and moments later was fortunate not to collect a second for a poor challenge on the same player on the edge of the home box.
The game changed again in the 68th minute when Clemens Fritz needlessly fouled Drogba in the box.
Ballack took over spot-kick duties from Lampard and showed the England midfielder exactly how to do it by smashing the ball into the top corner.
Lampard was inches away from making it three when he hit the inside of the post with a shot from an acute angle, but the near miss mattered little as the fight had drained out of Bremen and they never looked likely to produce a meaningful response.