The trio had been named in manager Michael O'Neill's squad for Friday night's international at the Adana 5 Ocak Stadium.
A statement from the Irish Football Association said McAuley has withdrawn for personal reasons, while Brunt has a groin injury and tendonitis in his knee.
It added that O'Connor has suffered a thigh injury.
West Brom teammates McAuley and Brunt have been a key part of the NI squad and their loss is expected to severely weaken the side.
They played the full 90 minutes of Saturday's dramatic 2-2 draw against Chelsea.
Meanwhile the further absence of Rotherham midfielder O'Connor means O'Neill now has just 18 players at his disposal for the game in Turkey.
No replacements have been announced at this stage.