Five minutes before the break, Austria increased their lead to 3-1 as Florian Grillitsch finished low across Oliver Sail after a flowing movement pierced the New Zealand defensive shape.
The Austrians went 4-1 ahead 11 minutes into the second half, Markus Blutsch slotting home from the penalty spot after a foul in the area.
From that point New Zealand found a more rhythm in their possession and spent the majority of the last 30 minutes on attack with Brotherton pulling a goal back in the aftermath of a short corner with 20 minutes on the clock.
But despite getting the ball regularly into the Austrian area late in the game the home side couldn't find a finishing touch to cap off their dominance in territory on the scoreboard.
New Zealand now turn their attention to their FIFA U-20 World Cup opening match against Ukraine on Saturday 30 May at North Harbour Stadium.
New Zealand 2-4 Austria (half: 1-3)
NZL: Clayton Lewis 12', Sam Brotherton 70'
AUT: Bernd Gschweidl 5', 25', Florian Grillitsch 41', Markus Blutsch (pen) 56'
New Zealand: 1. Oliver Sail (GK), 2. Jesse Edge, 3. Deklan Wynne, 4. Sam Brotherton, 5. Adam Mitchell, 7. Bill Tuiloma (capt), 8. Moses Dyer, 9. Alex Rufer, 10. Clayton Lewis, 11. Matthew Ridenton, 16. Joel Stevens
Substitutes: 12. Nik Tzanev (GK), 13. Brock Messenger, 14. Andre de Jong, 15. Andrew Blake, 17. Te Atawhai Hudson-Wihongi, 18. Noah Billingsley, 19. Monty Patterson, 20. Stuart Holthusen, 21. Cory Brown
Coach: Darren Bazeley