Morgan insisted they can still take positives from the tournament with the World Cup in 2019 in mind.
Morgan believes his side, who had won all three of their group matches heading into this semi-final, will have learned valuable lessons from this campaign as they look to again win their first major 50-over title in two years' time.
"It was not over confidence".
In his coloumn on a foreign news website, the former English cricketer said that the speculations on the Cardiff pitch was disrespectful to Pakistan as the side played well and adapted to the conditions.
"(But) certainly, that hasn't gone to our heads at all".
"Coming from Edgbaston which was a good wicket to a used wicket, we didn't adapt very well", Morgan told Sky Sports. "It's a big challenge jumping from venue to venue but we're going to have to do that with the World Cup so it's important for us to go through games like today for our experience". "I think all the three games [against South Africa, Sri Lanka and England] are the best games when I was captain".
England faltered from 128 for two to lose their last eight wickets for just 83 runs in under 23 overs on a low, slow surface.
England have been anything but since the World Cup - they've played some fantastic one-day cricket, it has been a privilege to watch it.
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He said: "I think for the first part of our innings, we played pretty well". It's a big frustration because I think we've played some great cricket in this tournament so far, and we weren't anywhere close to it today.
There's a reason why Pakistan were being termed as "unpredictable" going into the Champions Trophy and they proved it today.
If this becomes a trend, England will start to develop a reputation, but I believe we are some way from that. "They have probably got 15-16 players who could fit into this team and do a fantastic job", he added. But the team management boosted us really well.
Unable to find the breakthrough, English skipper Eoin Morgan got Adil Rashid back into action, and the leg-spinner delivered on the very first delivery of his fourth over with the wicket of the risky Zaman, stumped by wicketkeeper Jos Buttler.
He adds it means the team are out of a tournament they could have won: "They had all bases covered: powerful batting and a bowling attack full of variety and wicket-takers - a team of match-winners".
'We were disappointed not to beat Pakistan because we had been playing well enough but we still have a bit of work to do.