MacGill advised selectors of his dilemma prior to their announcement of the Test and One-day squads for the tour starting on May 17 that he did not believe he could tour Zimbabwe and maintain a clear conscience.
Australia is due to play two Tests and three One-day Internationals in Zimbabwe.
Selectors on Wednesday named 20-year-old Victorian leg-spinner Cameron White as a surprise replacement for the experienced 33-year-old MacGill in the 13-man Test squad.
Cricket Australia (CA) chief executive James Sutherland said he had spoken to MacGill and understood his decision not to tour.
CA said MacGill intended to outline his reasons for not touring Zimbabwe after playing for his English county side Nottinghamshire against Durham in Durham on Wednesday.
"Looking forward, the Australian national selection panel will continue to operate under the policy brief of selecting the best available team to represent Australia," Sutherland said in a statement.
Sutherland said MacGill's decision not to tour Zimbabwe would not affect his chances of future selection for Australia.
But Sutherland said CA believed that playing against Zimbabwe was "appropriate for the continued development of cricket as a global sport".
"We go there to play cricket with other cricketers to fulfil our obligations to world cricket through the ICC (International Cricket Council) future tours program, and for no other reason," he said.
Chief selector Trevor Hohns said the MacGill withdrawal gives selectors a chance to assess White at a higher playing level.
"We were keen to take two spinners to Zimbabwe and given Stuart's unavailability for the tour, we now have an opportunity to look at one of our younger spinners," Hohns said in a statement.
"His form in the Pura Cup (Sheffield Shield) with both bat and ball was very good and we're looking forward to seeing him take the next step on the international stage."
In another significant selection, senior paceman Glenn McGrath returns to the Australian Test side after a nine-month injury layoff.
Of McGrath's comeback, Hohns said:"Glenn's 100 percent fit and ready to go so it's sensible that he returns to the squad given his prior status as the premier fast bowler in the world.
"With the short nature of the tour it's a good opportunity for Glenn to ease his way back into competitive cricket and it gives us an opportunity to assess how well he is going, view to the next 12 months, and what lies ahead for the Australian cricket team."
All-rounder Andrew Symonds and young paceman Shaun Tait were left out of the Test squad, which claimed a three-nil series clean sweep in Sri Lanka last month.
All-rounder Shane Watson has been recalled to the One-day squad following a lengthy back injury.
Watson will get the opportunity to play his first Limited Overs match for Australia since the 2002-03 domestic One-day series.
The Test squad will depart for Zimbabwe on May 13.
Australian Test squad: Ricky Ponting (captain), Adam Gilchrist (vice-captain), Jason Gillespie, Matthew Hayden, Simon Katich, Michael Kasprowicz, Damien Martyn, Glenn McGrath, Justin Langer, Darren Lehmann, Shane Warne, Cameron White, Brad Williams.
Australian One-day squad: Ricky Ponting (captain), Adam Gilchrist (vice-captain), Michael Clarke, Jason Gillespie, Brad Hogg, Ian Harvey, Matthew Hayden, Michael Kasprowicz, Damien Martyn, Glenn McGrath, Darren Lehmann, Andrew Symonds, Shane Watson, Brad Williams.