Morgan was rested for the final game of the three-match series in Cardiff on Sunday with the score tied at 1-1.
Jos Buttler took over the captaincy but former England skipper Michael Vaughan responded to the decision by tweeting: "1-1 ... Series decider ... and the England Skipper is resting !!!!!!!!!!!!! #WTF ..... Worlds gone mad."
But Morgan, who drew criticism for pulling out of England's tour of Bangladesh in October 2016 because of his fears over terrorism, said the South African series was an opportunity to blood youngsters.
"It's an important part of our development, and our success in 50-over cricket and T20 has been down to the strength in depth we've had in the side," Morgan told Sky Sports.
"We've always had a lot of competition in the playing XI.
"Ideally, yes (he would have played). Given the rotation system that we have had in the past, it's unfortunate.
"If it was a case where I could go on and captain, I would.
"It's a very difficult situation to be in. I love playing international cricket, but unfortunately that is the case today.
"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."
England start a four-match Test series against South Africa on July 6.
They also play the West Indies at home in Test matches, T20 and one-day internationals before heading to Australia this winter for the Ashes, although Morgan will not feature in the longest format.
"There's a rigorous Test schedule coming up," Morgan said.
"It is a big call. But we haven't been shy of making big calls in the past.
"To continue with the mentality of backing up exactly what we're saying reinforces confidence in the side."
