Williamson posted centuries at the Gabba and Waca, while Warner backed up twin tons in the first test with a knock of 253 in Perth.
Smith scored 138 in the second innings of the second test, seeing off a spirited New Zealand fightback.
South Africa face India in the third match of their four-test series in Nagpur later this month, when a couple of failures from de Villiers could spell the end of his time at the top of the rankings.
Ross Taylor, who scored 290 in Perth - the highest test score by a foreigner in Australia - jumped seven places into 10th spot.
Mitchell Johnson ended his 73-test career ranked ninth on the ICC's bowling charts and fifth on the allrounder rankings.
ICC TEST BATTING RANKINGS:
1 - AB de Villiers (899)
2 - Steve Smith, Kane Williamson (893)
4 - Joe Root (886)
5 - David Warner (880)
-AAP