In pursuit of a ground-record chase of 298 all out, after Shane Watson (143) and Michael Clarke (76) had shared a fourth-wicket stand of 163 in just 22 overs, England could not get competitive despite Ravi Bopara's 62.
Two run-outs, including Kevin Pietersen's for a golden duck in the first over, were no help to the home cause as they finished on 249 all out in 48 overs under lights at the Ageas Bowl.
They therefore ended a summer of Ashes success against Australia with a 2-1 defeat in a five-match one-day international series which was reduced by rain to just three completed fixtures.
While Australia can therefore head home - or to the Champions League - with a belated success under their belts, Morgan must accentuate the positives provided by youngsters Jos Buttler, Ben Stokes and Chris Jordan as well as England's former Ireland fast bowler Boyd Rankin.
Debutant Jordan took three for 51 at Southampton; Stokes finished with a maiden five-wicket haul at this level - and wicketkeeper-batsman Buttler added another innings of 42, as well as five victims behind the stumps, to his two previous half-centuries in the series.
Morgan, standing in as captain for the rested Alastair Cook, said: "The biggest 'positive' is that we've got to see a lot of young cricketers come through, and we've got to learn about them more than anything.
"We've seen them perform at this level, which is great, against a strong Australian side.
"Here, Jordan looked really threatening up front. He bowled a heavy ball, and came back at the end and bowled well.
"He, along with Stokes, has impressed - and Rankin similar."
Morgan acknowledges the emerging quartet may not yet be about to replace the more established names, given a breather for this end-of-season series.
But he believes they will add vital strength in depth should wear and tear takes its toll on others by the time England face their next ODI assignment - against Australia again, in January.
"It's very difficult to ease (Stuart) Broad, (James) Anderson out of a team.
"But it's very important we have this depth throughout our squad, especially coming into an Ashes series and then the one-dayers after it.
"Anything could happen in an Ashes series - you could have a couple of guys go down, and potentially a couple of these guys coming in and replacing them.
"This series was about educating them and having a look at them. So it's a huge 'positive'."