Stokes intervened with two wickets on his return to the international stage, only for a stand of 178 between Ross Taylor (113) and Tom Latham (79) and then some late hitting from Mitchell Santner to get the Kiwis home with four balls to spare in pursuit of 284-8.
England will doubtless be relieved merely to have their go-to match-winner back in harness after his five months of unavailability following his arrest last September after a late-night incident outside a Bristol nightclub.
Stokes was restricted to 12 runs in half-an-hour of batting as Jos Buttler (79) and Joe Root (71) held sway - and then eight handy overs, returning with the wickets of Latham and Colin de Grandhomme in an unscripted second spell which could not quite prevent New Zealand’s ninth successive ODI win.
Chris Woakes put New Zealand’s reply in early trouble when Colin Munro became his’100th ODI scalp, edging behind on the charge.
Kane Williamson went caught-behind, too, opening the face to David Willey, and Woakes doubled up when Martin Guptill drove straight into Stokes’s hands at cover to make it 27 for three.
Taylor and Latham responded impressively, and with one moment of telling fortune for the latter on 48 when Buttler dropped a graze off the face of the left-hander’s bat from an Adil Rashid leg-break.
It was Stokes who gave England a chance again, Latham mistiming a smear to mid-on - and when de Grandhomme was caught-behind off a slower ball, the equation got to Taylor, stumped off Rashid - before Santner had the final say with 45 off only 27 balls.
England’s innings was stop-start throughout.
Like New Zealand’s chase, it began with a maiden - but it also contained seven overs from 42 to 48 which brought only 31 paltry runs when the late surge should have been truly on.
It did not help that they began the last 10 with five down - and even accounting for one of the deepest batting orders in world cricket, Buttler could not quite gather the expected momentum.
He took seven balls to get off the mark, yet then hit Ish Sodhi for three booming driven sixes in three balls.
Buttler counted two successive sixes again during the last two overs, but could not break the shackles in between.
Root, meanwhile, was guilty once again of failing to turn another impressive half-century into three-figures when there was ample time to do so.
He provided the thrust in a second-wicket stand with Jason Roy, after Jonny Bairstow had edged an early drive to slip off Trent Boult.
Even with some help from the field, though - Root, Roy and Buttler all either dropped or escaping a run-out - none could take full advantage.
Stokes was also granted a second chance on two, to little avail, when Boult put down a sharp return catch in his follow-through.
Roy was beaten in the air by Santner, bowled leg-stump one short of his 50; then Stokes joined Root after Eoin Morgan chipped Sodhi’s googly straight to mid-off.
Unwelcome anti-climax was visited twice in quick succession, Stokes contriving an edge to short third-man when he went to slog-sweep as soon as he first faced Mitch Santner, then Root missing a heave at Munro and bowled off-stump.
Moeen Ali threatened to play a big hand. But when he mistimed Sodhi horribly to cover, it was left to Buttler to eke out what he could.
In the end, it was not quite enough.