Neil Dunn and co-driver Mark Coventry brought their 2007 LandCruiser home first in the A1.5 class, while John Moralee and co-driver Greg Flood were victorious in the A0.3 class.
The two WA-based crews finished seventh and 10th overall in the nine-leg event that started in Kununurra on 24 August and finished in Perth on 1 September.
The Safari tackled Western Australia's most-diverse conditions, with auto and motorbike teams visiting tropical, dessert and forest terrain.
The Safari is Australia's version of the gruelling Paris-Dakar, an event that Toyota also enjoyed considerable success in earlier this year.
LandCrusiers filled the top-four places and seven of the top-10 in the T2 category.
Toyota's class wins in the Safari come just days before two more Toyota off-road teams tackle the Taupo 1000 - New Zealand's major off-road endurance event.
Two teams from the United States have entered the Taupo event in Toyota FJ Cruisers - a US-sold retro-style 4WD based on the Prado.
One of the teams will be the Toyota/Millen Works crew led by Ryan Millen, son of expat New Zealand motorsport star Rod Millen, a long-time Toyota driver and five-time winner at the famous Pikes Peak hill climb course in Colorado.
Ryan Millen's FJ Cruiser made its race debut in last year's edition of the legendary Baja 1000 off-road endurance race, where it finished second in the mini-stock class.
The two US-based FJ Cruiser teams will be followed by a large production team including helicopters, film-makers and media who will be making a one-hour sequel to their 2006 documentary - Two Roads to Baja.
The documentary followed the adventures and misadventures of the two teams while they were competing in the Baja 1000.
The Taupo 1000 runs from 8-9 September in New Zealand - and is quite unlike off-road endurance races in the US that are held in dry desert areas.
Competitors will cover up to 500 kilometres each day in conditions that could include sleeting rain, thick dust and occasionally snow.