The All Blacks lock was supposed to fly to Brisbane on Friday to start two weeks in hard quarantine, after remaining behind in New Zealand for the birth of his third child.
New Zealand Rugby (NZR) was only granted an exemption for Whitelock to quarantine in Queensland late on Friday, with his flight delayed until Tuesday.
NZR believe the timing of Whitelock's arrival would not give him enough time after two week's hard quarantine to safely prepare to play against South Africa on October 2.
He will now remain in New Zealand and will rejoin the All Blacks squad for their northern hemisphere tour.
However All Blacks first-five Richie Mo'unga will fly to Queensland on Tuesday and will be available for their final Rugby Championship test against the Springboks.
Mo'unga, like Whitelock, didn't travel with the the All Blacks to Australia last month as he too took parternity leave.