With Tottenham Hotspur drawing 3-3 at FC Twente to win Group A, Inter go through as runners-up, but Bremen remain bolted to the foot of the table as they picked up only their first win of the competition in sub-zero weather.
Not even victory here could lift them to third and a Europa League place for 2011, but a shot count of 20-6 in Bremen's favour told its own story and may once again reignite the debate over the future of Inter coach Rafael Benitez.
"We can be very pleased," said Bremen director of sport Klaus Allofs. "In the second half, the team went up a gear. Regardless of how tough the group was, it is annoying that we are no longer in the tournament."
Goals either side of half-time by Austrian defender Sebastian Proedl and compatriot Marko Arnautovic sealed the win against Benitez's lacklustre Italians before sub Claudio Pizarro added the third near the end.
"It was hard for us to react after the first goal, we had a few young players out there and they found it tough going," said Benitez. "The first goal hurt us and we didn't have many chances to get back in the game after that."
With Inter jetting off soon to the Club World Cup in Abu Dhabi later this month, Benitez said his priority is to get some of his injured squad back as quick as possible.
With the defending champions already through to the knock-out stages and Bremen playing only for pride, chances were few and far early on for either side on a bitterly cold night.
The brightest chance of the first half for Bremen came after 30 minutes when midfielder Aaron Hunt fired in a pass which striker Hugo Almeida volleyed, but Inter goalkeeper Paolo Orlandoni palmed the ball over the bar.
But Bremen poured on the pressure and camped in the Milan half until the opening goal came.
Having earned seven corners without reply, Bremen made the seventh count when centre-back Proedl rose highest and headed home on 39 minutes. Bremen made sure of the victory when striker Arnautovic latched onto a superb pass from Almeida and volleyed home his shot on 49 minutes which gave Orldoni no chance.
By this stage, the visitors were playing most of the football in their own half.
Inter won their first and only corner after 65 minutes and it nearly paid off as Argentinian midfielder Esteban Cambiasso's shot hit the post, but deflected back into play.
Bremen kept their foot on the gas until the final whistle and both Hunt and Arnautovic wasted chances. Both ex-Manchester United defender Mikael Silvestre and former Chelsea striker Pizarro came on late in the game after recovering from back and leg
It was Pizarro who netted the final goal in the 88th minute to end his team's European sojourn in style.