The 2019 World Cup hosts have just a few days to recover from a stunning one-day international defeat before they face title-holders Australia in the first of a five-match series at The Oval on Wednesday.
But having seen England beat Australia 4-1 in an ODI series Down Under earlier this year, captain Morgan was confident this loss would not do lasting damage to England's morale.
"A one-off game like this, to bring your best game is very difficult to do, they played well and deserved the result," said Morgan.
"It's not the end of the world for us, it was a really good run out and good to have a practice coming into the series against Australia.
"The level of expectation has been high around the team for a while, it doesn't get higher than being number one in the world.
"I don't think we were far away, we go to a ground now that we know really well in The Oval, and we'll be up for the challenge."
Morgan, however, accepted they had been well below the standard needed to win in what was their first 50-over match of the British season.
"We were miles off where we expect to be and didn't do enough to win," he said.
"The way we played, we didn't deserve to win it. We might have scraped past them and won, but there were still quite a few mistakes made that we need to rectify and learn from ahead of the Australia series.
Scotland's momentous victory came in their very first match since they were denied a place at next year's World Cup barely three months ago.
A combination of a controversial umpiring decision -- with no review system in place -- and rain saw them just miss out in the qualifying tournament in Zimbabwe.
The International Cricket Council had already angered Scotland and many of their fellow non-Test nations by cutting the number of teams at next year's World Cup from 14 to 10.
Former Durham and Warwickshire batsman MacLeod said Scotland's first international cricket win over England was a "massive statement".
He added: "It does not take away what happened in Zimbabwe and everyone's feelings about the 10-team World Cup but this was a special day.