Melbourne: South Africa fittingly finished their tour of Australia with a win as Amla's 97 inspired the tourists to a 39-run victory in the fifth and final one-day international at the WACA.
The win, South Africa's sixth during a historic tour Down Under, condemned Australia to their biggest ODI series losing margin on home soil and ensured the Proteas take their place as the top-ranked one-day nation.
The 4-1 series triumph was completed after half-centuries from Amla, AB de Villiers and JP Duminy saw South Africa rack up 288-7 - the ninth highest ODI total at the WACA.
In response, Mike Hussey struck a spirited 79 for the hosts and Brad Haddin blazed a quickfire 63, however four crucial wickets from debutant Lonwabo Tsotsobe resulted in Australia falling 39 runs short of their target.
Fielding three new faces from the side which crushed Australia by eight-wickets at Adelaide on Monday, the Proteas replaced star batsman Jacques Kallis, and pace pair Dale Steyn and Makhaya Ntini as Vaughn van Jaarsveld and debutants Tsotsobe and Wayne Parnell took to the field.
After winning the toss, captain Johan Botha gave openers Herschelle Gibbs and Amla first use of another hard and bouncy Perth wicket, however Australia struck early.
The dangerous Gibbs, who had laid the platform for victories with explosive innings' in Sydney and Adelaide, made just seven before he skied a Ben Hilfenhaus delivery to James Hopes at mid-off.
Then Neil McKenzie, promoted to No.3 in place of Kallis, failed to cash-in on his opportunity when he became Hopes' first victim of the day - edging through to Haddin for 10.
At 58-2 de Villiers joined Amla in the middle and the pair picked up where they left off in Adelaide as they effortlessly added 118 - their second consecutive century partnership - for the third wicket.
Both men registered fifties in less than 70 balls faced and Amla looked well set to become the first player to bring up three figures in the series.
Stand-in wicket-keeper De Villiers fell for 60, unfortunately picking out David Warner on the square-leg boundary after hooking a short ball from Hopes.
With Amla just three runs away from a second ODI century, the elegant right-hander played a loose drive off Hopes and Haddin pounced to hand the Queenslander his third scalp of the day.
Despite the double setback, the impressive Duminy fired off a classy innings at the death, scoring 60 off 42 deliveries as the Proteas powered to 288-6 from their 50 overs.
If Australia were to chase down the target, not only would they retain their No.1 status in one-day cricket, they would also break the record for the highest ever successful ODI run chase at the WACA.
Explosive openers Shaun Marsh and Warner strode to the middle hoping to exploit an inexperienced South African pace attack.
However, when Tsotsobe lured Marsh (5) into an uppish drive off his legs with his fifth ball in ODI cricket and Amla caught well, an uphill task became even steeper.
The left-armer continued to probe away and soon celebrated another prize scalp when he caught the edge of Ricky Ponting's bat and de Villiers snaffled behind the stumps.
And 35-2 soon became 35-3, vice-captain Michael Clarke continuing his poor one-day form when he shouldered arms to Morne Morkel and was clean bowled.
The aggressive Warner, playing his maiden first-class game at the WACA, showed glimpses of his ability with a towering six off Morkel, however his rapid 22 was cruelly brought to an end when Parnell deflected a straight drive from Hussey onto the stumps at the non-striker's end.
Hussey brothers Mike and Dave fought back bravely with a stand of 69 for the fifth wicket, only for the latter to throw away his start by driving straight to Botha off the part-time off-spin of Duminy for 32.
Undeterred, brother Mike took up the mantle expertly, caressing five fours and bludgeoning one six enroute to a 96-ball 78.
His innings gave Australia a glimmer of hope, and when Haddin produced a late flurry of boundaries the Perth crowd began to sense a dramatic comeback.
The Aussie gloveman eventually departed for 63 - Australia's eighth wicket to fall as Parnell claimed his first ODI wicket, and it was then left to Morkel to complete the win when he dismissed Nathan Bracken for just four.