Usman Khawaja and Glenn Maxwell were also among the run scorers, scoring 56 and 52 respectively, but it was former skipper Smith who was the star attraction.
While Smith played an attractive knock, Warner was out for a duck.
Smith, after being dismissed for 22 in his return to Australian colours on Monday after a year-long ban for ball-tampering, made the most of his opportunity in the second of three "unofficial" one-dayers in Brisbane.
Smith came to the crease when Shaun Marsh was out for 28 and was in fine touch, stroking an array of fours and sixes, in a major boost for Australia ahead of their World Cup defence in England.
Meanwhile, pace spearhead Mitchell Starc will make his long-awaited bowling return as New Zealand attempt to chase down 278 at Allan Border Field.
Starc has missed three months of cricket with a muscle tear, but was recalled for his first game since the Sri Lanka Test series.
Australia won the first of the three-match practice series, where games are not counted as full one-day internationals, by one wicket.