Alaba, the Bayern Munch midielder whose last-gasp strike in Dublin denied Ireland victory in March, repeated the dose 84 minutes into an encounter neither side could afford to lose to leave Austria clinging grimly to their hopes of claiming the runners-up spot in Group C.
That has now gone for Ireland, barring victories over leaders Germany and Kazakhstan by sizeable margins in their two remaining games and an unlikely series of results elsewhere.
While Austria possessed the greater craft with Alaba and sidekick Veli Kavlak pulling the strings in centre midfield, Ireland's more direct game repeatedly caused problems for the home defence. On several occasions, front two Robbie Keane and Shane Long got in behind the Austrian rearguard, but could not find the telling ball. But on a night when three points were a must even before Sweden had won in Kazakhstan earlier, the Republic were simply unable to find a way to win. Indeed, it was the home side who launched a late charge which eventually paid off with time running out.
Trapattoni's fate now likely to be sealed with his employers having demanded qualification in return for his £1m-a-year salary, and it remains to be seen whether he will still be at the helm for the trip to Cologne next month - for which central defenders Richard Dunne and John O'Shea will be suspended - after, remarkably, his first defeat in a qualifier on foreign soil.