Three days after their hopes of playing in Euro 2020 were dashed by Slovakia, it was generally a positive response from Ian Baraclough's side but, after Josh Magennis put them ahead, late goals from Louis Schaub and Adrian Grbic condemned them to defeat and almost certainly relegation.
Northern Ireland needed victory at the Ernst Happel Stadium to be sure of staying alive, with Romania expected to be awarded three points following the cancellation of their match against Norway due to positive tests for coronavirus in the Norwegian camp.
UEFA's control, ethics and disciplinary body is due to meet on Monday and Northern Ireland's fate should be known before they host Romania in Belfast on Wednesday.
Relegation under such circumstances would mark a new low in Northern Ireland's miserable relationship with the Nations League, a competition in which they have now lost eight of their nine games following Sunday's defeat, and a fresh setback after Thursday's heartache.
This defeat was as cruel as any that had gone before.
Northern Ireland showed spirit and energy in the wake of Thursday's extra-time defeat and were rewarded when Magennis fired them in front in the 75th minute, only for Austria to hit back twice in the last 10 minutes, with more than a hint of offside about Schaub's equaliser.
Austria's win, coupled with Norway's predicament, puts Franco Foda's side on course for League A as they moved three points clear at the top of the standings.
After 120 emotionally and physically draining minutes against Slovakia, Baraclough made eight changes for the match, handing a debut to St Johnstone's 20-year-old midfielder Ali McCann while switching the goalkeeper and his entire back four.
It was a positive start as the ball broke for Liam Boyce to run towards goal and the Hearts man fired a dangerous shot across goal, ignoring the option of squaring for Conor Washington.
The open start would not last, but the much-changed Northern Ireland side were certainly holding their own against more experienced opposition and posed a threat on the break.
Following the loss of Niall McGinn and Jordan Thompson on Thursday night, Shane Ferguson added to Baraclough's injury worries as he came off with a back problem in the 36th minute, replaced by Jamal Lewis.
Michael Gregoritsch, the scorer in Austria's 1-0 win in Belfast last month, headed narrowly wide from David Alaba's corner three minutes before the break, but the sides went in still goalless.
Frustrated by Northern Ireland, Foda made changes at half-time, pushing Alaba further forward, and the hosts gradually began to build momentum in the second half.
Baraclough made positive changes too, with Magennis and Gavin Whyte replacing Boyce and Washington.
But, just as Austria seemed to be taking control, Northern Ireland took the lead.
A neat passing move ended almost in slow motion, Austria's defence stepping up to try to catch Magennis offside. The Hull forward stood flat-footed as Paddy McNair side-footed the ball through but quickly came alive to fire beyond Pavao Pervan.
Northern Ireland's lead lasted only six minutes, however. A cross into the box took a touch off Grbic before falling for fellow substitute Schaub.
There were suspicions of offside as he turned it in but, with no VAR in place, the goal stood, and the turnaround was complete six minutes later when Arnautovic fed Grbic who fired beyond Michael McGovern.
To complete the misery, Northern Ireland assistant coach Austin MacPhee was sent off in the final moments.