Ireland were within a minute of securing a precious victory which would have propelled them into second place in Group C when the Bayern Munich man smashed an injury-time equaliser past goalkeeper David Forde to snatch a point which left his side in pole position to claim the runners-up spot instead.
It was a devastating conclusion to a tight encounter for the Republic, who dragged themselves back into the game after falling behind to Martin Harnik's cool 11th-minute strike. Jon Walters levelled from the penalty spot and then headed Ireland in front at the end of the first half - and it was a lead they were to defend doggedly until the final throes. A second draw in four days leaves Trapattoni's men knowing they face an uphill task to reach the play-offs.
They were ultimately made to pay for sitting back and defending a narrow lead rather than attempting to build upon it, a failing which will provide the manager's critics with further ammunition. Much of the pre-match debate had centred around Trapattoni's decision to select Derby County striker Conor Sammon as the injured Robbie Keane's replacement ahead of a series of seemingly better-qualified options.
Ireland spent much of the 20 minutes or so chasing shadows as Zlatko Junuzovic, Veli Kavlak and Harnik, prompted by Alaba behind them, repeatedly played their way through the green shirts. Alaba had whistled a second-minute free-kick just wide of Forde's right post to serve warning of their intent and the keeper was left cruelly exposed nine minutes later as Austria took the lead. Junuzovic caught central defender Ciaran Clark in possession and headed into the box before squaring for Harnik, whose first touch and deft finish gave Forde no chance.
Ireland's attempts to drag themselves back into the game were tame with James McClean, who had prospered early on, finding himself confronted by two men every time he received the ball. However, the Austrians having benefited from Ireland's generosity, returned the favour when central defender Emanuel Pogatetz misread Shane Long's intentions inside the box and brought him down. Referee Marijo Strahonja pointed straight to the spot and with no Keane in the side, Walters stepped forward to smash the penalty low to keeper Heinz Lindner's right to level.
Long was desperately unfortunate not to give the Republic a 38th-minute lead when he cheekily back-heeled McClean's cross towards goal, but saw his effort come back off the foot of the post with Lindner beaten. However, Trapattoni's men did go ahead in first-half injury time when Walters got ahead of marker Christian Fuchs to head firmly home from Glenn Whelan's inswinging corner.
Ireland start the second-half strong
Ireland very nearly extended their lead within two minutes of the restart when Fuchs was penalised for an untidy challenge on Sammon and McClean curled a free-kick inches wide of the near post and into the side-netting.
Trapattoni's men were starting to dominate, but they were reminded that there was no room for complacency as Austria responded in determined fashion. First Harnik forced a smart 54th-minute save from Forde after turning full-back Marc Wilson and the same man provided an inviting cross seconds later and looked on as full-back Gyorgy Garics volleyed across goal and wide of the post with the keeper stranded. Ireland had rather lost their way once again as they were starved of meaningful possession, although the resilience which has been their trademark for much of Trapattoni's reign to date was much in evidence as the hour-mark came and went without further mishap.
Indeed, the home side might have increased their lead twice within seconds when Lindner managed to keep the ball out of his net after McClean's 67th-minute cross was bundled towards his own goal by one of his defenders amid a melee in front of him, with Marc Wilson heading wide from the resulting corner. But Ireland dropped ever deeper as the game crept towards the final whistle and although they enjoyed a let-off when Harnik headed weakly at Forde with a minute of normal time remaining, the respite proved temporary.
The home side were camped inside their penalty area with seconds of added time to play when Alaba picked up possession 20 yards out and smashed an unstoppable shot high into the net to break Irish hearts.