Morgan wanted to give another opportunity to middle-order batsman Liam Livingstone who made 16 on debut in England's three-run defeat at Taunton on Friday, a result that saw South Africa level the series at 1-1.
But Morgan's absence also paved the way for Dawid Malan to make a debut at No 3 and his fellow Middlesex left-hander responded with an impressive 78 in a total of 181 for eight after South Africa captain AB de Villiers won the toss and fielded.
Malan's innings was the highest score by an England batsman on Twenty20 international debut, topping the 46 made by Paul Collingwood in England's very first match at this level - a 100-run win over Australia at Southampton in 2005.
During the course of Malan's 44-ball knock, featuring 12 fours and two sixes, Morgan - watching from the boundary at Cardiff's Sophia Gardens - told Sky Sports: "He looks very relaxed.
"He's been around a long time and scored a lot of runs at Middlesex in all three forms.
"We've given him an opportunity today and part and parcel of him developing is taking that opportunity," added Morgan, who at 30 is only a year older than Malan
Livingstone, however, fell for a golden duck clean bowled by paceman Dane Paterson as he attempted an extravagant ramp shot.
From 166 for three, England lost five wickets for 14 runs – a slide that Morgan, a veteran of 69 T20 internationals - might have done something to stop if he'd been playing in this match.
Earlier, Morgan explained the decision to drop himself by saying: "We recognise the series as a big opportunity to have a look at a younger group of players.
"If it was a case where I could go on and captain, I would. But this is an important part of our development for this series."
Former Ireland international Morgan added: "It’s a very difficult situation to be in. I love playing international cricket, but unfortunately that is the case today."
He insisted: "We remain very confident we can win the game with the team we have and put on a real entertaining show.
"It’s tough, but it’s a call you have to make looking to the long-term. It’s down to the quality of players that we have.
"It is a big call. But we haven’t been shy of making big calls in the past."