The listing, traditionally reserved for heritage buildings and homes, shows the cultural importance of the site, which is one of the most visited areas in Fremantle, attracting thousands of fans every year.
Kim Haynes, the National Trust's WA heritage officer, said Mr Scott's place in the annals of Australian and international music meant his gravesite deserved recognition.
"Normally people associate heritage with buildings, and this was a way of recognising the social values of a place. Heritage is about what we value," Mr Haynes said.
"This is very much a modern day pilgrimage for many, many people, and (the grave) is the end of pilgrimage for many people around the world."
Mr Haynes compared Mr Scott's memorial to another famous lead singer, whose grave had become iconic and much visited.
"We were able to make a very clear association with the phenomena of Jim Morrison's grave," Mr Haynes said.
"For that particular form and style of music, AC/DC were very significant in bringing that kind of music to the world."
Calls for a statue
The heritage listing comes as WA fans continue in a campaign to have a statue honouring Mr Scott, an effort backed by Fremantle's mayor Peter Tagliaferri.
Mr Scott was born in Kirriemuir, Scotland, but emigrated to Australia at the age of 6.
He grew up in Perth, first learning the drums and bagpipes for a local Scots pipe band. He dropped out of school at 15 and spent short spells in Fremantle prison and the Australian army.
Mr Scott joined AC/DC in September 1974 and, aided by regular appearances on ABC TV's music show Countdown, the band became one of the most popular and successful acts in Australia, before breaking into the international market.
Mr Scott was found dead in a friend's car in the early hours of February 19th, 1980, after a night of heavy drinking in London's Camden Town. He was 33.