South Africa's pacemen duly cashed in, with Kagiso Rabada (four for 39 in nine overs) and Wayne Parnell (three for 43 in eight) running through the top order.
On pacer Chris Woakes's fitness, Morgan added: "It is unfortunate that Chris Woakes limped out". Top-ranked South Africa lost their three-match series to England 2-1 but former ICC Under-19 World Cup star Rabada's haul of four for 39 in the final match at Lord's on Monday helped him finish the series with seven wickets and become the youngest number-one bowler since Pakistan's Saqlain Mushtaq in 1998.
Morgan, however, said Roy will keep his place in the team for England's next match against New Zealand in Cardiff on Tuesday.
"It is a great statement of intent and it fills us with confidence going into the next game".
Liam Plunkett (four for 59) was England's banker with the ball here, after Woakes left the field having bowled only two overs, but a longer-term replacement may well be required over the next two-and-a-half weeks.
Peter Moores was sacked as head coach soon after and the appointment of Trevor Bayliss has transformed England's fortunes in white-ball cricket, so much so that they will start the Champions Trophy among the favourites. "He's putting a lot of pressure on, and that's what we want".
Roy's opening partner Hales and Root went about their business without taking too many risks and ended up stitching a 159-run stand at little over run-a-ball. Needing to score more than six an over, the pair ensured England were never behind the eight ball. "It's the hardest thing telling Jonny he's not playing and he's done nothing wrong".
He added: "It's an odd injury, because everything he does - apart from bowl at 100 per cent in the game - is fine; when he bats he's fine, when he bowls he's fine, when he kicks a football around in the morning he's fine. He's a very important part of our side".
Other innovations at the Champions Trophy include the use of high-technology drones to provide more in-depth pitch analysis and a virtual reality system that allows fans to experience what it's like to face the world's best bowlers.
Morgan, however, is adamant there is no room in England's first XI for Bairstow at present. "We're very confident", he said.
The ICC Champions Trophy 2004 victor West Indies will not feature in 2017 tournament for failing to bag the spot among top eight teams in ICC ODI rankings by September 30, 2015. You can get out in that sort of fashion when you're short on runs.
Just like Sir Ian Botham and Andrew Flintoff, Stokes is an all-rounder who can not stay out of the spotlight, and this summer's Champions Trophy will be no different.
Woakes, who came into the match following a thigh problem and could now be replaced by next-in-line Steven Finn if this side strain proves serious, was not the only injury worry for England, with Root hobbling during his 10th one-day worldwide century.