England v South Africa: Scores and match report
All-rounder Stokes, making his return to the side after his MVP-winning turn in the Indian Premier League, left the field during the second innings after experiencing pain in his left knee and, though he later returned to the field, he did not add to his two overs.
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.
Stokes underwent an operation on the same knee exactly a year ago and concern is natural given his importance to England's Champions Trophy push, but Morgan appeared relaxed after the game.
"When he came back on the field he was fit to bowl, but we managed to take a wicket when he came back on and I felt bowling him again, even though he was fit, wasn't worth the risk...give him an extra day or two with ice," said Morgan.
"It doesn't even have swelling, no significant signs of an injury, but we'll assess that in the next couple of days. He did the right thing, went off to get checked, because knees can leave you out for up to six months or a year if something significant does happen.
"He came back on with the green light to bowl and was running around, but he understands. He's an experienced campaigner."
Minor nerves over the condition of the team's key all-rounder were outweighed by the satisfaction of piling on 339 for six against the number one ODI side in the world - then dismissing them for 267.
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.
"It was the best way we could have started, a very good day at the office and a pretty complete performance," he said.
"It's very satisfying putting in a performance like that, especially against a really, really strong team and given the start they got and the calibre of batting all the way down the order."
On Moeen's performance, Morgan added: "If he didn't get any runs and had a bad day, I'd probably pick him again.
"I have that much confidence in the guy. He's made some huge contributions for us over the last couple of years and beyond that.
"The fact he missed the Ireland games and comes back in and puts in a performance like this sums up him as a character.
"He's had a fantastic day and huge credit to him."
South Africa skipper AB de Villiers admitted the game got away from his side in the first innings after he won the toss and put the hosts in.
"England played phenomenally well with the bat, credit to Morgs for the hundred," he said. "They dominated the bowling and manipulated us, probably 20-30 above par and we didn't bat well enough. But congrats to them.
"We couldn't get a partnership going and at the end of the day we were outplayed."
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