South Africa's 88-run win will take them to top place in the International Cricket Council one-day rankings.
"We follow the small processes and if you do that the rewards come your way," said South Africa captain AB de Villiers. "I'm very proud of the way we performed.
"It's an important year for us with the Champions Trophy and regaining the No.1 position is a step in the right direction."s.
Sri Lanka captain Upul Tharanga admitted: "It's been a tough tour, right from the Test series (which South Africa won 3-0). It's a very young team and the players will learn a lot from this. The South African team played really good cricket."
De Kock batted with sublime skill as he made 109 off 87 balls while man of the match Amla scored 154 off 134 deliveries as South Africa piled up 384 for six after being sent in to bat.
The match was quickly over as a contest as Sri Lanka slumped to 82 for five.
But Asela Gunaratne hit 114 not out, his maiden one-day international century, to enable Sri Lanka to recover some pride at the end of a one-sided series, finishing with 296 for eight.
Gunaratne and Sachith Pathirana (56) were batting when an approaching storm caused de Villiers to get his spinners to rush through some overs in order to make sure 20 overs were bowled so there could be a result in the event of play being washed out.
As it happened the storm passed and the South Africa bowlers were unable to regain the ascendancy they held earlier.
"We wanted to bowl first and there was dew on the grass which made it difficult with ball in hand towards the end," said De Villiers.
Fast bowler Chris Morris took the first two wickets and finished with a career-best four for 31.
It was South Africa's 11th successive one-day win and their second successive 5-0 triumph after they beat Australia by the same margin earlier in the season.
Man of the match Amla was content to play the supporting role in an opening stand of 187 with De Kock, a record for South Africa against Sri Lanka.
"When Quinny gets going it's nice to watch from the other end. I was happy to play the passive role," said Amla who has hit four centuries in his last four innings at Centurion.
After reaching his hundred off 112 balls, Amla went on the rampage to score another 54 runs off 22 balls as he added five sixes and three fours to the 12 boundaries he hit in reaching his century.
Faf du Plessis was named man of the series after scoring 410 runs at an average of 102.50 with a strike rate of 105.
"When you're in a purple patch you have to make it count," he said.
centurioncricketHashim Amlaodi seriesQuinton de KockSouth AfricaSouth Africa vs Sri Lanka 2016-17sri lankasupersport park
First Published: February 11, 2017, 9:11 AM IST