The only cloud on the horizon as England went 1-0 up in a three-match contest ahead of next week's Champions Trophy tournament on home soil was the sight of Stokes leaving the field during the second innings after suffering pain in his left knee.
Stokes, in his first England match since his most valuable player-winning stint in the lucrative Indian Premier League competition, came back on later Wednesday but did not add to his tally of two overs.
Stokes had surgery on the same knee last year but Morgan insisted all was well with his star all-rounder.
"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.
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"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."
Morgan's innings and an unbeaten 77 from Moeen Ali, with the two left-handers sharing a century stand, helped England pile up 339 for six against South Africa.
- 'Best way to start' -
They then dismissed the Proteas for 267 with five overs to spare, Ali winning the man-of-the-match award after taking two wickets with his off-spin.
A delighted Morgan added: "It was the best way we could have started, a very good day at the office and a pretty complete performance.
"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," the former Ireland batsman added.
Wednesday's match took place just two days after a suicide terror attack in nearby Manchester that killed 22 people and injured dozens more.
Reflecting on his own performance, the often overly modest Ali added: "I backed my game today more than I have done in the past sometimes."
Meanwhile South Africa captain AB de Villiers said his side had been unable to contain an England team who plundered 102 runs from their last 10 overs after he had sent them into bat.
"England played phenomenally well with the bat, credit to Morgs for the hundred," said de Villiers.
"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."