Wolves striker Kevin Doyle has been called up to replace the Ireland captain after a scan on his calf injury this afternoon
Keane did not participate in Ireland training on Sunday at Gannon Park in Malahide as he reported for duty with a calf strain following Friday night's 0-0 draw with Sweden in Stockholm.
Despite being initially optimistic that the 32-year-old would be available for the crunch Austrian clash on Tuesday, Trapattoni has been forced to concede that he will be planning without his skipper following a scan on the injury.
A statement from the Football Association of Ireland on Sunday afternoon confirmed Keane's absence.
Kevin Doyle, originally omitted from Trapattoni's 23-man squad for the two matches, has been drafted in as a replacement.
The FAI has also confirmed that Doyle had been spoken to by Trapattoni and will link up with the squad on Monday morning for service.