No international team had ever chased down that many runs at SuperSport Park before as De Kock and Amla both hit centuries to trump Joe Root’s career-best 125 earlier in the day.
Morgan was naturally frustrated to see his side’s series lead cut to 2-1 – ahead of Friday’s fourth match in Johannesburg – and felt the game started to slip away in the early overs with the ball.
“It’s obviously very disappointing. To post 300 was a huge positive for us, our batting unit seems to go from strength to strength,” he told ecb.co.uk.
“Certainly at half-time we went in and thought we were right in the game.
“The learning curve from this game is how we started with the ball. We probably didn’t bang out line and length enough so it’s a matter of working on our basics and re-engaging with our basics next game and then the last game in Cape Town.”
With batting records tumbling across the world in limited-overs cricket in recent times Morgan knows that there will be some days his bowlers come in for punishment.
The 29-year-old is determined nonetheless to keep standards high to reduce the number of those days.
“I think it’s the nature of one-day cricket and T20 cricket. It’s a matter of trusting your bowlers and setting a plan and hopefully the plan will be executed,” he added.
“Today we didn’t do it as well as we have in the past but we haven’t got far to look as to where we need to make up the difference between the games.”
Morgan also called for his batsmen to take note of how South Africa ran down the target.
England have shown their ability to reel in big scores in the past year – most significantly when they pulled off a record chase of 349 for seven against New Zealand at Trent Bridge last June – and Morgan wants that to become the norm.
“Once the two openers managed to get away from us their experience kicked in and it is a little bit of a lesson for our team as to how they went about the chase,” he said.
“We’ve chased down large totals in the past and we’d like it to become a habit.
“You could see the experience in the South African unit that it has become a little bit of a habit. They’ve come back quite strongly.”
Root’s innings provided yet more confirmation of his class as he found a way to score big runs when the pitch was at its most difficult during the day.
“(It was) very important. Joe along with Jos is one of two senior players within our group and two great leaders within our group,” Morgan said.
“When Joe scores runs we do normally win so it’s obviously very disappointing not to win today but to score in the manner that he did today was brilliant.”
England will now make the short journey south for the fourth match at the Wanderers knowing that they still have two chances to win the series to go along with their Test success.
England have never managed a Test-ODI double on a tour of South Africa before although such an achievement is far from Morgan’s mind.
“I think it is important for us to focus on the processes rather than the outcome,” he said.
“We can get carried away with ourselves being 2-1 up. It’s important to re-engage with exactly what we’re doing well.
“We did that today with the bat and hopefully we do it in the fourth and fifth game with the ball.”