The Germans, who beat Bordeaux to win the trophy in May, were caught in an unexpected backlash to Valencia's current troubles. They have made a poor start to their domestic season and their preparations for the game were disrupted by a row that followed the decision by their coach, Luis Aragones, to drop the Brazilian striker Romario.
It looked like being more of the same for the local supporters when Scholl, Klinsmann and Rizzitelli all had chances to put Bayern in command in the first quarter of an hour, but a dubious penalty in the 19th minute, converted by Vicente Engonga, triggered a spectacular Valencia revival.
Six minutes later the Argentine striker Claudio Lopez made it 2-0 from a cross by the Russian midfielder Valery Karpin. Gabriel Moya headed home the third from another Karpin cross just after half-time with the Germans in disarray.
On a soggy Spanish night, Bayern's misery was completed by the dismissal of Alexander Zickler in the closing minutes.
In the Nationwide First Division, Barnsley maintained their 100 per cent record with an impressive 3-0 victory over Stoke City, who had begun the night two places behind them in third. Steve Davis, Neil Thompson - from 30 yards - and Andy Liddell scored the goals.