Shane Watson hit an impressive 143 runs from just 107 balls, and aided by Aussie captain Michael Clarke’s 75, helped the tourists finish on 298 all out with the series tied 1-1.
England bowler Stokes and Jordan took a combined eight wickets, but Morgan’s men struggled with the bat as Australia bowlers Mitchell Johnson and James Faulkner disrupted the hosts’ rhythm.
Ravi Bopara top-scored with 62, but the hosts eventually fell 49 runs short of the required target as Australia secured a ODI series triumph to provide consolation for their Ashes loss earlier this summer.
“We’ve been competitive. We’ve learnt a lot about guys coming through, especially Stokes, Jordan and Rankin. They showed a lot of promise. We’ve learnt they can step up to the mark,” Morgan told BBC Sport.
“The nature of the international schedule is that it’s hectic. We prioritise Test cricket and with back-to-back Ashes series we have to be picky and choosy. But the next best guys here have done really well.
“I’ve enjoyed being captain, giving caps to the younger guys coming through and the challenges of managing an inexperienced side.”