Hugo Almeida"s fourth minute goal gave Werder brief hope, but Miroslav Klose was sent off after only 19 minutes to make a tough job even harder for Thomas Schaaf"s team.
Espanyol will complete an all-Spanish line-up as they face Sevilla, who beat Osasuna 2-0 (2-1 agg), at Hampden Park in Glasgow on May 16th in only their second ever final. Their last appearance in the showpiece was in 1988.
Werder's Portuguese striker Almeida instilled early hope for the Bremen faithful when he benefited from a midfield scrap won by Diego as the battle lines were drawn.
The ball spun through to him, and spotting Gorka Iraizoz off his line he then beat Marc Torrejon to the ball and lifted it over the advancing Espanyol &lsquokeeper to give his side a 1-0 lead on the night.
Klose could have given the Weserstadion something to really cheer on 11 minutes when he took the ball down inside the area and was poised to shoot, but a great covering tackle from Daniel Jarque denied him at the crucial minute.
The Werder striker's red card came in the 19th as he was shown his second yellow card for a terrible dive under a tackle from Torrejon just outside the Espanyol area. His first booking came after only two minutes for an elbow on Jarque.
Torrejon made a clear effort to retract his leg and did not make sufficient contact with Klose to merit the way in which the German international flung himself to the ground.
French referee Bertrand Layec showed no hesitation in presenting the striker with his marching orders and Werder were reduced to ten men with barely a quarter of the match played.
Pablo Javier Zabaleta was unlucky to receive a mark against his name in the offical's book in the 26th minute when he was pulled up for tugging Diego's shirt. The real offender, Antonio Ito, managed to avoid punishment.
Werder, despite their numerical deficiency, pushed their guests hard, but could not find the net again before the break. Petri Pasanen went closest to reducing the aggregate score further when he volleyed inside the area. His effort lacked enough power to trouble Iraizoz and it was a single goal that separated the sides on the night at the break.
Espanyol crushed Werder's hopes of a complete turnaround though when they scored five minutes into the second half.
An Albert Riera cross was spilled by Andreas Reinke – filling in for the suspended Tim Wiese who was sent off in the first leg – and that left Corominhas with a straightforward finish into a partially guarded goal.
That finish all but sealed Werder's exit from the tournament, but Lacruz's header from a corner ten minutes later put a German recovery beyond doubt. The Espanyol right-back rose at the far post to beat Daniel Jensen and nod the Spanish side into a 2-1 lead.
The remaining half hour saw the Germans playing for pride, and Diego forced a good save from Iraizoz with a powerful volley in the 63rd minute.
Christian Schulz blazed a long-range shot over with two minutes of the match left, but by that stage it was apparent that Espanyol were to be the victors, and the final whistle confirmed the result to send Ernesto Valverde's men through.