The Leeds United man is selected to replace the injured Glenn Whelan, after the Stoke City midfielder was forced to withdraw from the squad with a hamstring injury.
Trapattoni's one other change from the side who were beaten 2-1 by Sweden on Friday night sees Norwich City winger Pilkington set to make his first start, taking the place of Wigan's James McClean after making his debut as a substitute last time out.
The Ireland boss acknowledged the need to pick up three points against Austria but stressed that there were three games left to play and plenty for which to fight.
"We know the only objective is win," Trapattoni told reporters. "Only with this result we can keep our hopes alive but we still have three matches."
