But barring the brief De Villiers fireworks, South Africa's reply was poor - only their captain and JJ Smuts (29) managed double-figure scores from their top six - with the writing on the wall somewhat as early as the second over when Reeza Hendricks departed for a five-ball duck, tamely chipping Tom Curran (2-22) to the man at mid-off.
Liam Dawson smashed the penultimate ball for a one-bounce four but the final delivery from the South African seamer beat Dawson and the tourists levelled the three-match series at 1-1.
But Roy and Jonny Bairstow kept the run chase motoring along, guiding the hosts to 92-1 at the halfway stage of the innings - meaning 83 were needed from the final 60 balls.
But Morgan's absence also paved the way for Dawid Malan to make a debut at number three and his fellow Middlesex left-hander responded with an impressive 78 after South Africa captain AB de Villiers won the toss and fielded.
"I didn't think (the chance) would ever come but nice to show what I can do".
The Protea players now had their tails up and they got another wicket when Phehlukwayo removed the unsafe Jos Buttler for 10 which gave them a real chance in the game.
The series concludes at Cardiff on Sunday. "We let it slip there".
Jos Buttler, standing in as captain for the rested Eoin Morgan, paid tribute to Malan's knock, while also praising the character of 20-year-old leg-spinner Mason Crane (1-38), who came in for some punishment at the hands of AB de Villiers before snaring the South Africa captain for his first worldwide wicket.
Sebastian Vettel and Lewis Hamilton in F1 crash row
Vettel, who is chasing a fifth world title to stop Hamilton winning a fourth, was given a 10-second time penalty for the incident. But unsurprisingly the stewards took a dim view of his desperate actions and ordered Mercedes to haul their man in for fix works.
Jason Roy, dropped on nought, fell for eight when caught behind trying to ramp fast bowler Morne Morkel.
His exit brought in Malan.
Malan, British born but rained in South Africa, follows Crane, Liam Livingstone and Tom Curran in making his debut in this series.
Hales had reached eight when he was struck on the knee by Paterson and left in a crumpled heap on the floor.
Man-of-the-match Chris Morris praised the character of his side after he inspired a fightback that saw England collapse from 133 for two to 171 for six.
JJ Smuts responded well to his golden duck in Wednesday's series opener to strike some lusty early blows, and it took the introduction of Curran to make the breakthrough as he struck with his second delivery in global cricket to dismiss Reeza Hendricks for seven.
De Villiers, in his last match of the tour - he is not staying on for the Test leg as he takes a break from the demands of playing all three worldwide formats - looked in good touch as he twice hoisted Crane for legside sixes in the 11th over.
Hales had made 36 from 28 balls when David Miller caught him on the mid-wicket boundary off Phehlukwayo.
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