The Sydney Cricket Ground will play host to the first two T20s, followed by the Manuka Oval, with the Melbourne Cricket Ground set to host the final two games.
The series, which begins on Feb. 11, previously included Brisbane, Adelaide and the Gold Coast as the other venues.
"CA will continue to prioritise the health and safety of all players, match officials, staff, fans, broadcasters and the wider community as we navigate the challenges presented by Covid-19," said Cricket Australia (CA) CEO Nick Hockley.
"We know that fans in South Australia and Queensland will be disappointed to miss out on these matches and we remain committed to bringing international cricket to all states."
On Wednesday, New Zealand's limited-overs tour of Australia was postponed indefinitely because of uncertainty over when the visitors would be able to return home due to COVID-19 protocols.