Leeds midfielder Paul Green replaces Glenn Whelan, who picked up a hamstring injury in the 2-1 defeat to Sweden, while Norwich's Anthony Pilkington comes in for James McClean on the left side of midfield.
Pilkington came on as a late substitute on Friday but will now make his first start for Trapattoni's side in Vienna.
Jon Walters (ankle) and Shane Long (dead leg) retain their places in the starting line-up after shaking off injuries.
The Republic must beat Austria and then win at group leaders Germany to keep their hopes of reaching next summer's finals alive.
But Trapattoni has already indicated that he expects to lose his job after this campaign.
Republic of Ireland team to face Austria: Forde, Coleman, O'Shea, Wilson, Walters, Green, McCarthy, Pilkington, Keane, Long.