On a day of six dropped catches by South Africa, it was Stokes who made them pay most heavily with his second one-day worldwide hundred - along with Jos Buttler's 46-ball 50 and telling runs too from Eoin Morgan - as England recorded four half-century stands.
The Proteas, already defeated in the series after England won the first two matches, made an incredible start with opening bowlers Kagiso Rabada and Wayne Parnell after captain AB de Villiers won the toss and elected to field at Lord's on Monday.
Jonny Bairstow's 51 and his two handy partnerships alongside David Willey (26) and Toby Roland-Jones, an unbeaten 37 on his debut, ensured a packed house were not home in time for lunch but the manner of the top order's subsidence must give them food for thought. During the tournament, de Villiers led South Africa to the semi-finals scoring 138 runs in four matches. For South Africa, Kahiso Rabada bagged four wickets.
It was 20/5 and officially a crisis as Jos Buttler followed up a boundary off Rabada with a drive that allowed Faf du Plessis to bag an excellent catch at second slip.
His aggressive approach is one that has served him well in all formats, as he showed with a blistering 258 from 198 balls against South Africa at Cape Town in a Test match past year. Stokes' first delivery saw Maharaj draw a thick edge, only for Amla to miss it completely at slip; then de Kock could not hold a more hard opportunity, again off the outside edge of the bat.
With overhead conditions providing just a touch of assistance for the seamers early on, England had struggled through the initial Powerplay.
Yesterday's performance - skittled out for 153 and slipping to a seven wicket defeat confirming a 2-1 series win - was the worst for some time.
Things could only get better for Stokes, and they did dramatically: he reached his century off 77 balls with 11 fours and three sixes before being caught at long-off.
"We didn't play too aggressively - a lot of our shots were defensive - so a lot of credit goes to South Africa".
One of the finest batsman in the game right now, de Villiers is an integral part of the South Africa side. "Always a pleasure. Hopefully we can go into the Champions Trophy on a high". "And getting the MVP (most valuable player) is obviously something you strive for when you play in tournaments like that". The cloud cover at Lord's helped Rabada turn into a monster with the ball that saw England batsmen fall like a nine-pin. "We lost myself and Quinny together so it could have been easier, but we batted very deep".
"Moeen has pulled up really well; Ben could have played, but it was another day off his feet, and the two bowlers that missed out could have played but it would have meant they were worn out again. and we didn't want that going into Thursday's game".