They led 10-7 at the interval and, after dominating possession in the second period, a penalty with three minutes to go made sure of the victory at the Northland Events Centre in Whangārei.
It means Australia finish second in Pool A on eight points and will be in the last eight while, for now, Wales - on five points - must wait on other results over the weekend to find out whether they will progress.
Given that this was a match between seventh and ninth in the World Rugby Women’s Rankings powered by Capgemini, it was always going to be a tight affair.
It was Australia - coming in off the back of a victory against Scotland last time out - who started the stronger and they took the lead after just five minutes.
The five-pointer came through scrum-half Iliseva Batibasaga and when full-back Lori Cramer converted it was 7-0.
That was the way it stayed until the 24th minute when Wales hit back through a try from number eight Sioned Harries. It was converted by fly-half Elinor Snowsill and things were level at 7-7.
No quarter was being given by either side and, just before half-time, Cramer kicked a penalty to give Australia a crucial 10-7 lead at the interval.
Australia were trying to get their big ball carriers like captain Shannon Parry and number eight Grace Hamilton on the ball and in the 49th minute they nearly scored their second try of the day.
Fly-half Arabella McKenzie was held up over the try-line and the Welsh defence were continuing to do a very good job.
As the game headed towards the hour mark, Australia remained the team on the front foot and with the territory, but often when they tried to string phases together there was a handling error which stopped things in their track.
By the 65th minute Wales had made more than 200 tackles, but they were staying in the fight and frustrating Australia with consistently good defence.
With 11 minutes to go there was a decision for referee Sara Cox to make and, after speaking with the TMO and viewing footage, she gave Australia replacement Kaitlan Leaney a yellow card for a high tackle.
Wales, try as they might, could not capitalise on having an extra player and, eight minutes into the 10-minute sin-binning period, Australia scored the points with 14 players that clinched this important victory for them.
Cramer, as she has done all tournament, kept her cool with the boot and, back up to 15 players, the Wallaroos then managed the last couple of minutes well to get over the line.
Australia took four match points from this one and Wales one losing bonus point which could be crucial in the final reckoning.