The series win boosted South Africa's rating from 101 to 106 enabling it to climb above West Indies (105) and England (103) in the ranking release by the International Cricket Council on Monday.
England, which began the series in fourth place on 109 points, saw their rating falling by six points and has slipped to seventh in the table.
Former South African skipper Shaun Pollock jumped to second spot in the ODI bowling rankings, just three points behind Australian Glenn McGrath while Jacques Kallis slipped from top place in the ODI batting rankings. West Indies batsman Ramnaresh Sarwan took the top spot.
England veteran Darren Gough's excellent series saw him return to the bowling top ten - he finished in eighth place - while Kevin Pietersen's dramatic start to his ODI career took him to the 25th place in the batting rankings.
England's only batsman in the top ten is the injured Andrew Flintoff, with Marcus Trescothick dropping 15 places over the series to end in 20th place, ICC said in a release on Monday.