Jordan, who is a six-time NBA champion, majority owner and basketball operations manager of the Charlotte Bobcats, was due to be American captain Fred Couples' assistant at the tournament in Melbourne, but has now stepped down due to the ongoing NBA lockout.
"After careful consideration, it is with regret that I have decided to cancel my trip to Australia later this month for the Presidents Cup," Jordan said on Wednesday.
"With the NBA labour situation unsettled ... I feel it is necessary that I remain in the country.
"It was an honour to have been chosen by Fred Couples to serve as a captain's assistant. I wish Fred and the United States team the best of luck."
Couples wasted little time in naming 11-time PGA Tour winner John Cook as Jordan's replacement.
"I would like to thank Michael for his significant contributions, both as captain's assistant and his role as ambassador for the Presidents Cup," Couples said.
"While the team will miss his friendship, spirit and leadership, we certainly understand the complexity of his current team obligations."
The 2011 Presidents Cup is scheduled to start on November 17.