It's the third time in four years Lexus has taken out the title, winning in 2014 and 2015.
"At Lexus, we pride ourselves on producing passenger cars and SUVs that exhibit the finest quality and craftsmanship," said Peter McGregor, chief executive of the company's local arm.
"Just as importantly, we remain committed to building on the foundation of our business, which is to deliver an exceptional ownership experience."
Above: Lexus RX
This latest announcement comes after Lexus was the highest-ranked luxury brand in the 2016 J.D. Power 2016 Australia Customer Service Index Study.
The Roy Morgan Customer Satisfaction Awards are based on face-to-face interviews with approximately 50,000 automotive customers across Australia.