Bayern, who face Atletico Madrid in the Champions League last four next week and could clinch the Bundesliga as early as Saturday, will face either Borussia Dortmund or Hertha Berlin who play on Wednesday.
"We are under pressure in every game. We know that and we have to deliver," Mueller told reporters. "We had some problems tonight, we made too many mistakes, too many wrong passes."
"I won't talk badly about our performance because it is absolutely amazing what the team is delivering every three days."
Germany international Mueller scored with a bouncing header after Clemens Fritz slipped in the box, leaving the forward with a clear path in the 30th minute and with Bayern in complete control.
The hosts had little trouble against the former German champions in the first half, though the visitors did have one golden chance when Manuel Neuer left his goal but Sambu Yatabare's weak lob gave the keeper enough time to sprint back.
Bayern should have scored in the opening minutes of the second half with Werder attacking and leaving huge gaps at the back.
The risk, however, almost paid off on the hour for them with Bayern's David Alaba putting the ball into his own net under pressure from Fin Bartels, penalised for an offensive foul.
Minutes later the referee awarded Bayern a penalty with substitute Arturo Vidal diving and television replays showing no contact of the Chilean with Werder's Janek Sternberg.
Mueller stepped up and converted the spot kick, instantly dashing Werder's hopes of a comeback and turning the remainder of the game into a procedural matter.
(Reporting by Karolos Grohmann, editing by Alan Baldwin)
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