De Villiers, 29, hit a fighter 164 in the second Test against Pakistan in Dubai. He and skipper Graeme Smith, who made 234, put on 338 – a South African record for the fifth wicket – and the S.Africans won the match by an innings and 92 runs on Saturday.
De Villiers was also declared Man of the Series.
Amla missed the Dubai Test after returning home for the birth of his child.
West Indian Shivnarine Chanderpaul is third in the batsmen’s rankings.
Smith returned to the top ten of Test batsmen after his monumental 234. The South African skipper jumped seven places and is now eighth in the rankings.
De Villiers, who had scored a fighting 90 in South Africa’s seven-wicket defeat in the first Test in Abu Dhabi, earned 27 points to go past 900 points in the ratings, the ICC said.
He is the fifth South African and 28th batsmen in the world to reach 900 rating points. Before him Dudley Nourse, Graeme Pollock, Jacques Kallis and Amla were the other South Africans to achieve the distinction.
Smith’s twin, Misbah-ul Haq achieved a career-best sixth spot after scoring a century in Abu Dhabi and a fighting 88 on Saturday.
Dale Steyn of South Africa remains the world’s best Test bowler according to the rankings.
South Africa remains the world’s best Test team followed by Ashes winners England and by India.
Pakistan moved up to fourth in the Test team rankings after sliding to sixth following their embarrassing defeat against Zimbabwe last month.