The 31-year-old broke the news of his withdrawal on Twitter, admitting that he is "absolutely gutted" to miss the tournament.
He wrote: "[I] am absolutely gutted, out of the Games due to injury. Best of luck to everyone at Glasgow, I'll defo be there cheering you on."
Austin was one of five Olympians to make the Scottish judo squad, and was due to compete in the 100kg weight class alongside teammate Euan Burton.
Judo will return to the Commonwealth Games at Glasgow 2014 for the first time since 2002.