Hosts Juve needed just a draw to qualify on Tuesday and went ahead through David Trezeguet's 19th-minute strike.
However, Bayern stormed back thanks to a penalty from goalkeeper Hans Joerg Butt and goals from Ivica Olic, Mario Gomez and Anatoliy Tymoshchuk.
"The coach is not in danger. Ciro is and remains the coach of Juventus," club president Jean Claude Blanc told reporters on Wednesday. "We move forward with our project."
A catalogue of disapponting signings have undermined Juve's return to the upper echelons of European football following their Serie A demotion for match-fixinig in 2006.
Jorge Andrade, Christian Poulsen, Tiago, Sergio Almiron all struggled while Brazilians Diego and Felipe Melo were booed in Tuesday's defeat after again failing to live up to their billing following big close-season moves.
Rookie coach Ferrara, whose side lost at Bordeaux in their previous Group A game and now drop into the Europa League, refused to blame the duo.
"We share the responsibility. Those two (Brazilian) players are new. But we mustn't hide behind excuses," he said.
"In the last two matches we haven't done anything to deserve to go through. Bayern were the superior side. They played like a great team and we had lots of problems."
ATTACKING LINEUP
With media reports saying Italy coach Marcello Lippi will return to Juve after the World Cup in some role, Ferrara's long-term future is unclear.
Van Gaal's prospects are much brighter after his side's display followed a sticky start to the season in Europe and the Bundesliga.
Needing a win to go through, Van Gaal went for broke with an attacking lineup.
"We've played the last few games with the same side so if we were scouted I don't think we could have surprised Juve so much," said the Dutchman.
"We just simply played really well and in the dressing room afterwards all I said was 'well done and let's continue like this'."
The coach had no qualms about keeper Butt taking the 30th minute spot kick which levelled the scores at 1-1.
"I have a hierarchy for who takes them but Butt was in the best condition so I let him take it," he said.
