Hard work ahead for Magath and his men
A 41,300 crowd at the Zentralstadion in Leipzig saw Munich open brightly, but referee Manuel Gräfe wrongly disallowed a Lukas Podolski effort midway through the half.
The Reds faded rapidly after that and Croatia striker Ivan Klasnic's well-worked opener came as no real surprise, prompting Felix Magath to make a raft of changes for the second half.
The five-times League Cup winners continued to struggle for a response as the combination of intense preseason training, a level of fitness some way below normal levels and an unfamiliar formation took its toll.
There was no way back for the Bavarians once Klasnic had doubled the advantage from a 66th minute free-kick, and Magath will have been particularly concerned at his side's inability to convert any one of their 13 shots on goal. Five days to find form
Just five days remain until the Bundesliga opener at home to Borussia Dortmund on Friday, and the champions will be keen to put right the drought which has seen them fail to score from open play in their last three friendlies.
Magath's starting lineup reflected the club's continued search for a new shape in the post-Ballack era.
Martin Demichelis was sidelined but Oliver Kahn and Lucio returned from rest and injury to give the back four a relatively first-choice feel.
The experimentation continued elsewhere though, with Owen Hargreaves in his favored holding role, Roque Santa Cruz entrusted with the so-called 'Ballack position' behind the strikers, and Ali Karimi making a start on the right. Podolski denied
Munich had the better of the early exchanges in a relatively entertaining encounter, but the match officials denied the Reds what would have been a psychologically important opening goal when Podolski was incorrectly ruled offside from Roy Makaay's intelligent layoff on 23 minutes.
Werder took full advantage when World Cup top scorer Miroslav Klose burst past two defenders and brilliantly released Klasnic to fire an unstoppable 15-yard drive past Kahn's left hand.
Magath withdrew battle-weary German internationals Lahm, Schweinsteiger and Podolski at halftime as the champions reshuffled in a bid to make good the 1-0 deficit. Battling Brazzo
Andreas Ottl, Hasan Salihamidzic and Julio dos Santos entered the fray in defensive midfield, down the left flank and behind the front two respectively, with Hargreaves dropping to left back and Santa Cruz moving forward to partner Roy Makaay.
Salihamidzic in particular created havoc in the Bremen defense, but neither the Bosnian nor dos Santos forced Werder keeper Tim Wiese into a meaningful save.
The game was up after Klasnic drove his free-kick low and hard past a less than solid wall and into the bottom corner, and although Santa Cruz, Lucio and Salihamidzic all had chances, Kahn ultimately kept the score within reasonable limits with good saves from Schulz and sub Aaron Hunt as the northerners deservedly lifted the League Cup trophy for the first time.