The selectors had delayed Johnson's departure from Perth to link with the squad, hoping he would recover sufficiently from a toe infection ahead of Australia's campaign which opens against Pakistan on March 23.
But they decided today he had run out of time and opted for a cautious approach with the summer's superstar, replacing him with 32-year-old Bollinger.
Johnson has been on a course of antibiotics to treat the infection from a cut suffered during the third Test win in South Africa in Cape Town.
"We have given Mitchell as long as we can but unfortunately his infection hasn't responded to the treatment as quickly as we had hoped with swelling remaining in his toe and foot," said CA's chief medical officer Dr Justin Paoloni.
"It is difficult to say how quickly the infection will take to resolve and due to the high risk of infection recurrence with a return to bowling we feel it is in the best interests of Mitchell's health for him to continue to receive intensive treatment in Perth."
However his call up is a blow to NSW who take on Western Australia in the Sheffield Shield final starting on Friday.
In this season's T20 Big Bash League, playing for runners-up the Hobart Hurricanes, Bollinger took just six wickets at an average of 44.66 and an economy rate of 7.65.
He has played only two T20 internationals, in South Africa in 2011, taking one wicket in each match.
In four ODIs in Asia, all in India, he has best figures of 5-35 and an average of 19.33.
His Shield return of 31 wickets at 24.09 had him drafted in Australia's Test squad during the Ashes series as cover for Johnson and Ryan Harris, but he was not needed as the squad remained unchanged while completing a five-nil whitewash.