The Norwegian won the final round of the 2016 season by 14.9sec from team-mate Sébastien Ogier, who spun away his own chances.
It provided a perfect farewell for the German manufacturer, which bows out of the series after a dominant four-year period.
Mikkelsen's win in a Polo R was not enough to secure the runners-up spot in the drivers' championship.
Third place for Thierry Neuville in a Hyundai i20, a further 57.7sec back, secured the position behind the already-crowned Ogier.
Ogier won the final live TV Power Stage to claim three bonus points.
Neuville took two points for second, while team-mate Dani Sordo secured the final point.
Kennards Hire Rally Australia (provisional):
1. Andreas Mikkelsen (Volkswagen) Total time 2hrs 26min 05.7sec
2. Sebastien Ogier (Volkswagen) Difference to first +14.9sec
3. Thierry Neuville (Hyundai) +1:12.6
4. Hayden Paddon (Hyundai) +1:26.7
5. Dani Sordo (Hyundai) +1:28.3
Drivers' standings (Provisional after round 13):
1. Sébastien Ogier 268 points
2. Thierry Neuville 160
3. Andreas Mikkelsen 154
4. Hayden Paddon 138
5. Dani Sordo 130