Amla achieved the feat in his 126th match and 123rd innings. Kohli had taken 144 matches and 136 innings to reach the same landmark.
The 32-year-old Amla has scored his runs at the terrific average of 52.70 and strike rate of 89.36.
As South African coach Russell Domingo reminded the media before the match, there are only two batsmen to have an average of 50+ in both Tests and ODIs and both of them are in the current South African side: Amla and AB de Villiers.
Amla also has 21 tons in those 126 games at an astounding ratio of one in every six games.
His average, however, has dipped during this series. He has scored just 89 runs in the five matches, his lowest in any ODI series in which he has batted for four or more innings.
South Africa will be hoping that Amla regains form before the Test series which kicks off on November 5 in Mohali.