Boegman, along with runners David Geddes and Katerina Dressler, pulled out of the team for the event, which starts in Manchester on 25 July.
Athletics Australia said the trio had been ruled out because of injuries.
Boegman won long jump gold in the 1994 Games at Victoria, Canada.
The 10-time national champion had failed to recover from an Achilles tendon injury, an Athletics Australia spokeswoman said.
Geddes, the 200m national champion, was withdrawn because of a stress fracture of the back.
Dressler, who claimed the 400m national title this year in the absence of Olympic champion Cathy Freeman, pulled out because of an unspecified medical problem.