Supercars co-driver Perkins posted a 1:31.04s on his final lap in the 15 minute session held in warm and dry conditions at the New Zealand circuit.
The duo have struggled to find the balance in the car and will start from 12th on the grid after missing out on Saturday's Top 10 Shootout.
Warm-up ran largely without incident although the #88 Peter Edwards/Graham Smythe Ferrari 458 GT3 escaped a wild spin at Turn 1 that saw car narrowly miss the barriers.
The pair ended the session in seventh behind the #1 Christopher Mies/Tony Bates Audi R8 GT3.
Greg Taylor and Nathan Antunes were eighth in their Audi R8, while the top 10 was completed by the Matt Simmons/Michael Caruso Nissan GT-R and the McElrea Racing Audi R8 of Simon Ellingham and Tim Miles.
Meanwhile, the Trass Family Motorsport Ferrari 458GT3 has withdrawn from the event.
The team suffered left rear suspension failure in Saturday's first qualifying that pitched Sam Fillmore into a spin.
It is hoped the car will be repaired in time for the Australian GT Endurance Championship Highlands 101 from November 11-13.
The Australian GT Hampton Downs 101 is scheduled to begin at 1145 AEDT.
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RESULT: Australian GT Hampton Downs 101 Warm-up