Warner left Australia in a winning position as it chased New Zealand's 281-9 when he put on 122 for the first wicket with Usman Khawaja, who repaid his belated recall to one-day cricket with a classy half century.
When Khawaja was out for 50 the Australia innings faltered and Warner saw four wickets fall for 22 runs, including captain Steve Smith (2) and George Bailey (0) to consecutive balls from Matt Henry.
Warner was out with Australia 90 runs from victory but Mitch Marsh led Australia to 283-6 with 3.3 overs to spare, making an unbeaten 69 in a record 86-run run stand with John Hastings (48 not out).
New Zealand beats Bangladesh by 8 wickets in 3rd ODI