Bayern battled to a 2-1 away victory on Saturday, with Arjen Robben's fine finish and David Alaba's stunning free-kick before the break proving decisive despite Max Kruse's second-half strike.
"It was difficult, but we deserved it," he said. "We got into some problems after the [Bremen] goal.
"Werder played very well, especially in the second half, but there are always difficulties during a season."
Robben, meanwhile, felt Bayern should have been much more dominant after establishing their two-goal lead, rather than allow the struggling hosts a way back into the game.
He added: "If you go 2-0 up then it must be game over.
"Bremen put us under more pressure in the second half, playing even more to the front, but then it has to be easier as more space is created for us.
"We have to play much better with more control of possession. If we had done, it could have actually been 3-0 or 4-0. Even in the first half we allowed too many counter attacks, so there is still a lot to improve. "
Bayern are back in action against Schalke at the Allianz Arena next Saturday.