The tourists can only draw the series now, with England 2-1 up heading into the final match at Lord’s on Friday. The teams shared their recent Twenty20 series 2-2.
Stokes, England’s Test captain, has made a seamless return to the ODI a year after retiring from the format because of what he described as an “unsustainable” schedule.
He made 52 in the first ODI and now has surpassed his previous best ODI knock of 102, making his fourth hundred in 93 innings in the format.
“He’s played a few good ones,” England captain Jos Buttler said of Stokes, who has starred for the country in the big games in all formats, “but that was amazing.”
Stokes’ spot in England’s team for the World Cup — as solely a batter — is guaranteed and so it appears is Malan’s after he came up just short of his fifth ODI century, when he was caught behind off Boult.
Elsewhere, there might be a few issues developing in the batting line-up three weeks out from the tournament.
Roy was absent again after having another back spasm hours before the match. The opener missed the first two games with the same problem and could now be a doubt for the World Cup.
Harry Brook, who is not in the provisional squad and is pushing to replace Roy or another batter, dropped out of the team to accommodate the return of Malan and has only made 25 and 2 in this series.
Meanwhile, Joe Root was dismissed for 4 to add to scores of 6 and 0 this series.
Also worrying Wednesday was the late-innings meltdown after Stokes’ dismissal when he was caught by Will Young at square leg off a full toss from pacer Ben Lister. From 5-348, England was all out 22 balls later for the addition of just 20 runs.
As for the Black Caps, they left out spinner Mitchell Santner after he jarred his knee fielding in the second ODI and were completely outplayed with bat and ball.
England and New Zealand meet in the first game of the World Cup on October 5.