Bastian Schweinsteiger's injury, Arjen Robben's loss of form and a dull goalless draw at Bundesliga strugglers Freiburg on Saturday combine to make Bayern look vulnerable.
Basel have already pulled off one shock this season by taking four points out of six from Manchester United in the group stages to qualify for the last 16 at the expense of the Premier League side.
The Swiss league champions also have inside knowledge of their opponents as coach Heiko Vogel spent nine years working with Bayern's youth scheme where he coached several members of the current team.
In another twist Basel winger Xherdan Shaqiri will be keen to show his future club what he is capable of, having already been signed by Bayern for next season.
Basel are unbeaten in 13 matches in all competitions, their last defeat coming at home to Benfica in the Champions League in early November when Vogel took over following the sudden departure of Thorsten Fink to Hamburg SV.
"It's special that there is Swiss involvement in the last 16, the fact I started my training career with Bayern makes it even more interesting," said Vogel.
"We have a small chance and we want to take it as we did against Manchester."
Basel, who also reached the group stages in 2002/03, could be rusty though as they have played only twice since the winter break.
Four-times European champions Bayern were almost untouchable earlier in the season but have struggled for form since the New Year.
The Bavarians have dropped from first to third in the Bundesliga, four points behind leaders Borussia Dortmund.
Dutch winger Robben has been left out by coach Jupp Heynckes and described as "selfish" by honorary president Franz Beckenbauer.
"When he has a good effort or scores a goal he does not run towards the player who set him up but instead he runs towards his family in the stands," said Beckenbauer. "He lets the team run after him."
Schweinsteiger, who usually runs the midfield, has been ruled out for several weeks with an ankle injury.
That is a severe blow to Bayern especially as he scored both goals in the 2-1 win at Basel in last season's group stages.
Schweinsteiger's absence was no excuse for Saturday's poor effort at Freiburg, according to sporting director Christian Nerlinger.
"We have to get our act together as fast as possible and present a different face," he said. "We need fundamental changes very quickly indeed or it'll be a very disappointing season."
Bayern however are still chasing a Bundesliga-German Cup-Champions League treble and the fact their Allianz Arena will stage the final of Europe's elite club competition is a huge incentive.
Basel: 1-Yann Sommer; 27-Markus Steinhoefer, 19-David Abraham, 6-Aleksandar Dragovic, 3-Park Joo Ho; 17-Xherdan Shaqiri, 8-Benjamin Huggel, 34-Granit Xhak
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