Hanley will take at least six weeks to recover and is considered doubtful for the World Cup warm-up matches with Canada and the United States in August.
Clive Woodward, the England coach, will almost certainly recall Hanley's club-mate, David Rees, to the right wing for the big date with the Wallabies. Dan Luger, who has just joined Saracens from Harlequins, is a certain starter on the left wing.
The 30-strong Scotland squad flies out for South Africa today with the coach Jim Telfer planning to use the tour to bring on his youngsters ahead of the World Cup.
Telfer, whose tenure ends after the World Cup, believes the trip "will make sure that the good work done in the Five Nations goes on. It will also be an opportunity to bring on a number of youngsters and at the same time allow several experienced players a chance to rest."
Among the latter group are flanker Peter Walton, prop David Hilton, lock Scott Murray and stand-off Gregor Townsend, while others like Kenny Logan and Alan Tait have been prevented from touring because of injury.
"We would have liked Alan to be on tour but unfortunately he suffered two injuries in the same shoulder. The second was not discovered until the first had mended," said Telfer, whose party also will be without Tait's centre partner, John Leslie, currently under contract to Japanese side Sanix.
Another aim, Telfer said, is the rehabilitation of a number of recent first-choice players such as Doddie Weir, Tom Smith, Matthew Proudfoot, Bryan Redpath and Duncan Hodge.