"It's a lesson with the bat and ball... our bowlers to be disciplined and to our batsman that, sometimes, you have to sit in," Morgan told reporters after the match.
"They made us play a hell of a lot and managed to get the ball moving around. Certainly, it's not down to a lack of trying."
England coach Trevor Bayliss believed that the humiliating loss would ensure his team remained level-headed for the eight-team Champions Trophy.
"This result ensures we go into the Champions Trophy without big heads," Bayliss told BBC's Test Match Special.
"We should have done better than we did but a 2-1 series over South Africa, we'll take that every day."
The victory was made all the more sweeter for South Africa batsman Hashim Amla, who became the fastest to break the 7,000-run barrier in one-dayers by reaching the milestone in just 150 innings, beating India's Virat Kohli by 11 knocks.
South Africa begin their Champions Trophy campaign against Sri Lanka at The Oval on Saturday.
(Reporting by Aditi Prakash in Bengaluru; Editing by John O'Brien)
