Sir Alex Ferguson's team are now in the Europa League after their shock 2-1 defeat at St Jakob Park stadium in their final group stage game last December saw them dumped out of the competition.
Basel coach Heiko Vogel, a self-confessed Bayern fan, is looking to give the Bavarians the same giant-killer treatment his team dished out to United with the return leg in Munich on March 13th.
"We don't want to just play well. We want to reach the quarter-finals," said Vogel, with his team six points clear at the top of the Swiss league.
"The task is even more difficult than against Manchester United.
"You just have to name some of their players.
"Once more, David fights Goliath.
"It will be very, very difficult to defy them for 180 minutes."
Vogel learned his trade in Munich and was a youth coach at Bayern for nine years until 2007.
Bayern won Group A convincingly with four wins, including a 2-0 home win over Premier League giants Manchester City, but their form in 2012 has left much to be desired.
"If we play like Man United did, we will also have problems," Bayern chief executive Karl-Heinz Rummenigge admitted.
Their goalless draw at Bundesliga bottom side Freiburg last Saturday saw the guests out-played in the first-half and their midfield is not so self-assured without ankle-injury victim Bastian Schweinsteiger.
As daily newspaper Bild commented, the screwed up face of Bayern president Uli Hoeness is showing the signs of a club in crisis.
Bayern have won just two of their five league games since Christmas and director of sport Christian Nerlinger admitted he was "mystified" by the lethargic performance at Freiburg which left them third in the German league.
Even Dutch winger and World Cup finalist Arjen Robben found himself in the unusual position of starting on the bench for the last two matches.
"We have to get our act together as fast as possible and present a different face," demanded Nerlinger.
"We need fundamental changes very quickly indeed, or it'll be a very disappointing season for Bayern Munich."
Munich will also be in the unusual position of facing one of their future players having signed Basel's 20-year-old attacking midfielder Xerdan Shaqiri, who joins Bayern as of July 1st 2012.
Basel lost 2-1 at home to Bayern last season in the group stages of the Champions League because of a last-gasp goal from Schweinsteiger, but without the Germany star, Bayern are a different prospect this season.
Coach Jupp Heynckes is taking nothing for granted in Basel.
"We must not forget that this team has prevailed in a very difficult group and has ousted Manchester United," he said.
"They have highly talented young players and an enthusiastic crowd. Also, they are a side with experience in Europe."