He cracked his eighth half-century but fell on 61.
But it was a different matter when Morgan went after Phehlukwayo, off whom he struck 42 of his runs and four of his sixes.
Stokes threatened to click into full gear when he drilled Kagiso Rabada down David Miller's throat in the deep for 25. At that stage England were 198/5.
Spinners Imran Tahir and JP Duminy had been a good bulwark but, after 46 balls without a boundary off their bowling, Morgan opened the floodgates with three in the space of six deliveries.
Such a costly collapse only got worse when Chris Morris, straight after hitting Moeen for four, attempted a reverse sweep and watched on in horror as the ball skipped up and comfortably into the waiting gloves of Buttler.
A collapse of the South African middle-order and a magnificent hundred from Eoin Morgan helped England overcome the Proteas by 72 runs in the first ODI at Leeds.
Hashim Amla got South Africa off to a steady start with a succession of glorious drives but Quinton de Kock toiled a little, before sending a steepler into the night sky that Buttler caught after scampering down to fine leg and practically barging Mark Wood out of the way. He is nursing a left knee injury.
Morgan, pipped to the man-of-the-match award by Moeen Ali's unbeaten 77 and two wickets, was a contented skipper as he reflected on the display.
But Amla again proved a thorn in England s side with a typically elegant near run-a-ball 73. Then in the very next over Morgan brought Plunkett back and he enticed an edge from Du Plessis for 67.
Despite a strong start in reply via Hashem Amla and Faf du Plessis, once they departed wickets continued to tumble at regular intervals.
Of particular concern for the Proteas is the fact that their hotel in Manchester - where the final Test will be played from 4 to 8 August - is within walking distance from the Manchester Arena, where the blast occurred and claimed 22 lives.
"It was a big shock and what happened is sad and unfortunate", De Villiers said.
Captain Morgan, who hit a decisive 107 to underpin his side's winning effort, revealed that Stokes had been cleared to bowl by medical staff but made the on-field call to keep him on the shelf with the game all-but won.