A dramatic batting collapse saw England lose their last seven wickets for just 14 runs as the Proteas made it two wins in the two-match T20 series, following on from their 3-2 victory in the ODI series last week.
Speaking afterwards, Morgan admitted that five successive defeats was hard to take but insisted that his team were "young" and "hungry" to learn and improve in the forthcoming World T20 in India.
"We have to take the good with the bad," he told Sky Sports News. "We are a very young and exciting team who on our day can beat any side in the world but we might also have a blip along the way with inexperience we have.
"When you are winning all the time you don't always appreciate it but now we are being tested so it is a good stage for us - how we come back from it is more important than anything. We were so far behind the eight ball at the previous World Cup that we have so much ground to make up as we try and play a brutal way, like South Africa do with bat and ball, and win a world tournament.
"We just haven't been good enough over the last few games and haven't deserved to win but we talk about it all the time and guys are hungry to learn, which is a good sign, so we are optimistic ahead of the World T20."
England's opening match in the tournament is against the West Indies in Mumbai on March 18, two days before they are due to face South Africa again.