Up against a Cricket Australia Chairman's XI side featuring several retired players and some fringe first-class cricketers, the Black Caps fell seven runs short in a big run chase, despite a century by new skipper Brendon McCullum.
After the home side was dismissed for 285 in 47 overs, the Kiwis made 9-278 from their 50 overs.
The Black Caps needed 15 off the last over to win.
The match offered New Zealand its only chance to tune up for Tuesday's sold-out Twenty20 international against Australia at the WACA Ground, and the subsequent three-match Chappell-Hadlee Trophy series.
With new skipper Daniel Vettori rested, McCullum took over the captaincy for the first time and led from the front, making 119 from 126 balls at the top of the order.
The gifted strokemaker hit nine fours and five sixes on the small Lilac Hill ground, but lacked support as the required run rate grew.
He was the only Kiwi batsman to make a significant score, although Jamie How and tailender Mark Gillespie both made 30.
The Kiwis looked set to win when McCullum and Matthew Sinclair (27) put on 57 for the fourth wicket, but the latter's dismissal to part-time spinner David Hussey sparked a collapse, with the Black Caps losing 4-45.
Star all-rounder Jacob Oram made just 12 and when he was stumped from the bowling of Hussey, New Zealand's hopes of victory were fading fast.
Hussey, young spinner Aaron Heal and retired seamer Jo Angel each claimed two wickets for the Chairman's XI.
Earlier, wayward Western Australian batsman Luke Pomersbach took to the New Zealand bowlers to belt 88 from 65 balls.
The big-hitting Pomersbach, dropped from the WA side recently for disciplinary reasons, was well-supported by Hussey, who made 73 from just 53 balls and hit five sixes.
Oram was the best of the New Zealand bowlers, with 3-41 from seven overs.
Chris Martin also impressed with 2-36 from nine overs, while Iain O'Brien claimed one wicket, but went for 52 runs from just four overs.