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Just hours after collecting a fourth Allan Border Medal on Monday night following a stellar 2012 campaign, Clarke was bumped down to No.2 as Amla made it a South African clean sweep of the test rankings.
Fast bowler Dale Steyn strengthened his lead at the top of the bowling list after claiming 11-60 in South Africa's first test win over Pakistan, while Jacques Kallis remains the game's preeminent all-rounder.
Amla's elevation to the No.1 test ranking makes him the first batsman since former Australian captain Ricky Ponting in 2007 to top both the test and one-day batting list at the same time.
"I am surprised and happy with my position as the No.1 ranked test batsman," Amla said.
"However, I'm also mindful that rankings change quite regularly.
"It's been a great year for our squad, and to be honest I still don't think that I am the best batsman in our team.
"What has been most pleasing though for us has been the all-round contribution from everyone in the squad that has been the main reason for our success over the last few years.
"... it is always easier to be at the top of your game and successful when you are part of a winning team.
"Dale and Jacques have been tireless workhorses for the Proteas and continue to consistently put in quality performances for our team, it is no wonder that they are at the top of the bowling and all-rounder rankings."
South Africa's standing as the dominant force in test cricket is reflected in the rankings, with AB de Villiers and Kallis joining Amla amongst the top ten batsman, while pacemen Vernon Philander and Morne Morkel are also in the top ten list for bowlers.
Clarke is the only Australian ranked amongst the top 20 test batsmen, with David Warner the next best at No.25.
Test spearhead Peter Siddle has moved up one spot to No.4 in the bowling ratings, with the injured Ben Hilfenhaus the next best Aussie at No.10.