Batting first, the Kiwis scored 347, with Paul Rugg top-scoring with 87, Richard Preston making 81 and Harley James hitting 46.
The Kiwis bundled out the home side for 75, with Wade Cornelius taking four wickets for 15 and Todd Harris three for 19.
Forced to follow on, the Emus reached 193 for seven by stumps on the second day.
After a rearguard action on the final day, the Canterbury bowlers dismissed the Emus for 262.
Cornelius picked up another four-wicket bag, giving him match figures of eight for 60. Harris (2-22) and Cleighton Cornelius (2-45) were other useful contributors in the Canterbury attack.