That defeat meant England had to be content with a 4-1 one-day international series win rather than a first home 5-0 whitewash.
It also denied Morgan's men, who back in June tied an ODI with Sri Lanka in Nottingham before winning that series, a maiden unbeaten season in white-ball cricket ahead of Wednesday's lone Twenty20 against Pakistan in Manchester.
England may still be fifth in the International Cricket Council ODI rankings but they have made significant progress since their embarrassing first-round exit at last year's World Cup in Australia and New Zealand.
"We've been outstanding," said Morgan. "Every game throughout the series, we've come out with a hunger and determination to perform at our best."
England fell short of what they wanted in making 302 for nine in Cardiff, with opener Jason Roy top-scoring with 87 and all-rounder Ben Stokes contributing an ODI-best 75.
But they were on course for a whitewash when Pakistan lost two wickets in one Mark Wood over to be 77 for three.
- 'Hunger' -
============
Morgan, though, remained heartened by England's commitment to an aggressive approach in ODI cricket since their World Cup debacle.
"I think it's exciting," he said.
"The attitude and hunger to want to be better playing in that manner, I think, sums up the direction one-day international cricket is going and the talent we have."
But with world number one-ranked Australia also completing a 4-1 series victory away to Sri Lanka on Sunday, Morgan denied England -- beaten on home soil in the 2013 final by India at Edgbaston -- were favourites for next year's Champions Trophy.
"I know the last Champions Trophy we played (here), the pitches were a bit drier than we thought, and brought in sub-continent teams.
Man-of-the-match Ahmed, who also scored Pakistan's first
ODI hundred at Lord's in the second match, was the leading overall run-scorer in the series with exactly 300 at an average of 60.
"The way Sarfraz batted, this whole tour he's been exceptional," said Pakistan one-day captain Azhar Ali following a much-needed win.
"He's been positive and scoring good runs at number five, so we've got some good performances but we just need to bind it together."
Azhar has often been compared unfavourably to celebrated Test captain Misbah-ul-Haq, who has led Pakistan to the top of the ICC standings in the five-day game.
But Azhar responded to suggestions he might resign the captaincy by indicating he intended to carry on as skipper.
"I got a few 80s (against England) so that will really help my confidence. Leading by example is very important. I will try and keep that form in the coming series. That will help the team."
"A few guys we have seen on this tour have really stepped up -- they are young guys, and if they can play good consistent cricket we are looking at a bright future.
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