Left-arm spinner Daniel Vettori and medium-pacer Chris Cairns claimed three wickets each as they put the clamps on Australian scoring in the middle of the innings.
Vettori claimed 3-31 from 10 overs and sparked a collapse with the wickets of Australian captain Ricky Ponting (29), Damien Martyn (1) and Andrew Symonds (0) to reduce the home side to 123 for five.
Darren Lehmann (50), Michael Clarke (36) and Brad Hogg (20 not out) led the Australian recovery, but the world champions had been on track for 300 before Vettori struck with a double-wicket maiden.
Vettori's three wickets in two overs steadied the Australian run-rate after Gilchrist again got Australia off to a flyer with 68 from 54 balls, with nine boundaries.
Gilchrist dominated a 64-run opening with Matthew Hayden, who fell for 13 to a sensational diving one-handed catch by Mathew Sinclair in the deep in the ninth over.
Ponting took some time to bat himself in and Gilchrist was bowled by Cairns trying to lift the scoring rate.
Vettori followed up his good Test form by removing Ponting and Martyn lbw to silence a crowd still on a high from Gilchrist's innings.
When Symonds drove poorly to mid-on and was caught for a third-ball duck, Australia had lost 4 wickets for 10 runs in 22 balls.
The collapse slowed the run-rate, as Australia managed just 25 runs in the middle set of 10 overs after being 117 for two after 20 overs.
Lehmann and Clarke ensured Australia batted through its overs, but wickets fell regularly and NZ captain Stephen Fleming's decision to remove his expensive opening bowlers Ian Butler and Kyle Mills with bowlers more suited to a slowish wicket paid off.
Cairns finished with 3-39 including the wicket of Clarke.
Lehmann brought up his half-century in the 45th over, but was out shortly after flicking Jacob Oram (2-51) straight to backward square.