Corry Evans' first international goal in eight years had cancelled out Xaver Schlager's opener and looked to have earned Northern Ireland their first point in the Nations League.
But Lazaro fired the ball into the top corner of the net after Stuart Dallas lost possession in another frustrating night for Michael O'Neill's men.
With Northern Ireland's relegation already certain following three straight defeats, there was a rather flat atmosphere in the ground which would soon be reflected on the pitch in a first half of few chances.
The hosts began brightly enough, with Liam Boyce using his physical presence to worry the Austria defence as he held the ball up.
When the Burton man was dispossessed six minutes in the ball fell for Corry Evans, whose deflected shot was touched over by the back-peddling Heinz Lindner.
But Austria were going into the game as they constantly looked for David Alaba down the left.
The Bayern Munich man curled a free-kick just over after being brought down by George Saville, although Trevor Carson looked to have it covered anyway.
There was a less certain moment for the Motherwell goalkeeper soon after when he was slow to get down to Michael Gregoritsch's low shot,despite a lack of power in the effort.
With Gareth McAuley back in the side, making his first Northern Ireland appearance since June, O'Neill's side were looking to profit from set-pieces.
But a Steven Davis free-kick looking for the Rangers man was cut out before the following corner somehow evaded several Northern Ireland players as it sailed across the face of goal.
As the half wore on both sides began to get bogged down in a midfield battle, with neither team able to create much.
A minute before half-time Saville won a free-kick on the edge of the area, but Niall McGinn's shot curled inches wide.
Austria needed just four minutes of the second half to break the deadlock.
Davis failed to cut out a low cross from substitute Peter Zulj as Alaba played a neat dummy and Schlager darted in front of Saville to arrow a shot in to the far corner.
The goal brought the match – and Northern Ireland – to life.
They launched a half-hearted appeal for a penalty when Jonny Evans tumbled over under pressure from Aleksandar Dragovic.
McGinn then drove at goal and played in Davis, whose low shot was blocked by Dragovic before McGinn fired over from the rebound.
And Northern Ireland were level in the 56th minute. This time it was Jordan Jones who strode towards goal before slipping the ball in to Corry Evans.
The Blackburn man took a touch to steady himself before striking a low shot which deflected off Martin Hinteregger to given Evans his first goal for Northern Ireland since 2010.
Schlager could, and probably should, have put Austria back in front in the 66th minute when he got a toe to Gregoritsch's shot, but he diverted it wide with the goal at his mercy.
Austria were enjoying another spell of supremacy, with Alaba – switched to the right wing – cutting inside before firing just wide from the edge of the area.
Marko Arnautovic then came on for the last 20 minutes and was soon involved as he laid the ball off for Alaba, but this time he blazed over.
Things began to get tetchy as the match moved into the final stages and McAuley was booked after appearing to hold Arnautovic in a headlock when they were on the floor.
But, just as it appeared Northern Ireland had earned a point, Dallas gave the ball away and Arnautovic played in Lazaro to deliver the final blow.