Smith achieved the feat during the second ODI against India at the Wanderers here yesterday.
Smith, who made his captaincy debut at the young age of 21 against India at Dhaka in 2003, has so far led South Africa to 139 ODIs, one higher than Cronje`s record.
"Graeme Smith`s achievement is outstanding, especially when it is taken into account that he became captain at the age of 21, only after one full season in international cricket," Cricket South Africa chief executive Gerald Majola said.
"Graeme has more than justified CSA`s faith in his leadership qualities when he was appointed at such a young age, and since then he has grown considerably in stature both as a player and as a captain.
"It is most fitting that he achieves this extraordinary South African captaincy record against India eight years later," he said.
Majola said under Smith`s leadership, South Africa has evolved a major force in world cricket
"He has been an essential part of the process that has moulded the Proteas into a formidable ODI unit, and the cherry on the top of his captaincy would certainly be bringing the ICC World Cup home," the CSA chief said.
"CSA salutes Graeme Smith for what he has done and will continue to do for the progress of South African cricket in achieving its aim of becoming a truly national sport of winners," Majola added.