England were reduced to 20 for the loss of six wickets inside the first five overs of the match in Middlesex, which is also Morgan's home ground in English domestic cricket.
Stokes, who briefly left the field with a knee injury in England's 72-run win in the series opener at Headingley on Wednesday, showed no discomfort with the bat, although he only bowled three overs.
England fought back through the recalled Jonny Bairstow (51), David Willey (26) and debutant Toby Roland-Jones (37*) while Keshav Maharaj bowled beautifully in the middle overs, picking up 3/25.
In the end, a total of 153 was achieved thanks largely to Jonny Bairstow, who further pressed his claims for a place in England's XI with a third half-century in four ODI innings, and a belligerent unbeaten 37 from Toby Roland-Jones on his worldwide debut.
Bairstow then gave his wicket away when he charged at Maharaj only to be stumped by de Kock to end a 67-ball knock featuring eight fours.
After two excellent performances to wrap up the three-match ODI series, England looked a shadow of themselves as they compiled a dire display against South Africa at Lords.
In response, South Africa got to the target in 28.5 overs (making 156 for three).
His aggressive approach is one that has served him well in all formats, as he showed with a blistering Test-match 258 from 198 balls against South Africa at Cape Town previous year. Australia's warm-up match against Pakistan only lasted a handful of overs and South Africa A again were only able to bat half an innings in their second warm-up match against Derbyshire. De Kock, who has had a phenomenal last 12 months, bagged the SA Cricketer of the Year, ODI Cricketer of the Year, Test Cricketer of the Year, SA Players' Player of the Year and the SA Fans' Player of the Year.
Gary Kirsten, South Africa's coach during their previous Champions Trophy campaign, in England in 2013, confronted the issue head-on by discussing the perception with his players, rather than having it as an unseen or unspoken elephant in the room. He's putting a lot of pressure on, and that's what we want.
"It is just in my delivery stride bowling", he said. "It was was disproportionately important (to win the toss) and went a long way towards deciding the game".
"We're constantly monitoring him and trying to manage him as best as we can", Morgan said.
"We had a lot to play for today, and there are some encouraging signs", De Villiers said.
Morgan was impressed by Bairstow but did not appear to echo Bayliss" sentiment, saying: "I was very impressed and as I continue to say he never lets us down.