The ratings were released on Tuesday.
Kallis, who made 147 and 49 in his two innings in the drawn Test against Australia last week, leapfrogged Shakib al Hasan of Bangladesh into the No. 1 spot.
Elsewhere in the rankings table, Dale Steyn and Vernon Philander were rated first and second respectively among bowlers, with fellow Proteas speedster Morné Morkel ranked ninth.
Hashim Amla remained South Africa's top-ranked batsman, in second position, trailing only Sri Lankan veteran Kumar Sangakkara.
Kallis was ranked third among batsmen, with vice-captain AB de Villiers (sixth) and captain Graeme Smith (10th) also in the top 10.
With Amla hunting top spot in the rankings for batsmen, just four points behind Sangakkara, South Africa will look to fill the number one position in all three divisions after they face Australia in the second Test starting in Adelaide on Thursday. – Sapa