Trapattoni had been planning to use a three-man midfield comprising Whelan, Keith Andrews and James McCarthy, but a hamstring injury suffered by the Stoke man against Liverpool on Sunday puts him on a lengthy absentee list that also includes Richard Dunne, Kevin Doyle, Sean St Ledger and James McClean.
The Ireland manager admitted that Whelan is the one player in the squad who he believes he doesn't have a natural replacement for, yet he delivered a strong hint that he will proceed with plans to use an extra midfielder to counter the substantial German threat at the Aviva Stadium. That would leave Trapattoni gambling with a straight choice between Birmingham's Keith Fahey and Sunderland's David Meyler for a starting role.
"It's a big loss," said Trapattoni. "And it's a bigger loss because of the opponent. Now, we have to decide what to do."
He rotated Meyler and Fahey in training yesterday, feeling that the latter has the edge technically whereas the former is more imposing physically. Usually, Trapattoni asks skipper Robbie Keane to drop a little deeper to support the midfield, but the 73-year-old has suggested he is thinking differently ahead of this encounter.
Shane Long will be kept in reserve with a view to being used as an impact sub in the second half.
St Ledger's unavailability means that John O'Shea will move inside to partner Darren O'Dea in the heart of the hosts' back four, with Stephen Kelly, Seamus Coleman and Paul McShane vying for inclusion at right-full.
Aston Villa's Ciaran Clark has been recalled from the wilderness to provide defensive cover.