"It's a defeat. You are never happy with defeat," Mourinho told reporters after the 1-0 away defeat to Werder.
"But it's a defeat that delivers us into the second stage of the competition."
Per Mertesacker scored Bremen's only goal when he beat compatriot Michael Ballack to head home a Torsten Frings corner-kick.
"We knew the most difficult situations would be the set pieces because they have four or five players (around) 1.98 meters or two meters tall and we only two or three players strong enough in the air to cope with it," Mourinho said.
"When a team has five players (around two meters tall) and another has just Ballack, John Terry and (Didier) Drogba, the other team will try to dominate every set piece."
Despite the defeat Chelsea have secured their place in the knockout stages and will play their last match against Levski Sofia with the sole objective of finishing the group as winners.
"In this very difficult group to be safe in the next round, to be comfortable, to be the first in the group, to be qualified is an achievement. That's very important."
When asked about the injuries that Ballack and Drogba picked up in Wednesday's game, Mourinho said: "Ballack's injury is nothing special. It is just pain, the opponent put his studs on his muscle.
"Didier is the same. He has a pain in the ankle but it is nothing serious."
But the former Porto manager had other concerns about Ballack.
"I don't think Ballack played a good game," he said.
"Sorry, but sometimes that happens. It's not a problem, he just didn't play a good game."