Australia captain Michael Clarke struck 105 as Australia posted 315 for seven in Manchester - their highest score against England in this country.
England lost early wickets in their pursuit of what would have been a record chase and never recovered to be bowled out for 227 from 44.2 overs.
"It was very disappointing," Morgan told Sky Sports.
"Not to get a win under our belt is disappointing but we can learn a lot from today. Moving on from here were are looking forward to Wednesday.
"We have a very strong batting line-up and one we have confidence in regardless of whether we bat or bowl first .
"We have a lot of bowling options and guys we can turn to. (Batting wise) there were not enough guys putting their hands up.
"We felt the lengths we tried to hit at the back end and middle period where Australia played really well and we just didn't cope well with the wicket.
"Unfortunately today we lost wickets at unfortunate times."
Man-of-the-match Clarke was pleased to claim a win following the 3-0 Test series defeat.
"It's a a nice feeling. The boys deserve credit as to make more than 300 on that wicket was a really good score and our bowlers executed well," he said.
"It doesn't matter how you win it's about crossing the line. As a one day outfit that's our goal. We are here to win the series and 1-0 is a good start.
"I always want more runs and hopefully this is the start of a few more during the series."
Clarke also played down the problems of balancing a side, adding: "It's always hard with every team. You want to have your cake and eat it, strengthen your batting and have an extra bowler.
"The guys in our changing room have so much talent, if they feel confident they can take a bowler no ground is big enough."