Ireland-born Morgan scored a century of his own as England set the visitors an imposing victory target of 329 at the Rose Bowl but he sat out the second innings because of a minor groin injury.
He watched on from the boundary as Stirling, who was dropped on 95 and 139, and Ireland captain Andy Balbirnie (113) put on 214 for the second wicket to help the Irish overhaul the target for a second victory over England in 12 attempts.
“Paul Stirling had a day out and he’s the ability to do that,” Morgan told reporters.
“But we play against world class players all the time and you know when you do, you need to take those opportunities because they will hurt you.
“Ireland played really well and thoroughly deserved to win.”
Defeat in the final over 😕Congrats @IrelandCricket 👏 Scorecard/clips: https://t.co/iWz8HBGPG6 https://t.co/J2yZRCgH7i
— England Cricket (@englandcricket) 1596574779000
Morgan briefly overlapped with Stirling in the Ireland set-up before switching allegiance but knows him better from their time as team mates at English county Middlesex.
“He’s as dangerous an opening batsman as there is around the world,” he said of the 29-year-old.
“I know guys do not like bowling at him, he hits good balls for four or six and, on his day, he can take a game away from you.”
Morgan, who was having a scan on the groin “tweak” but did not anticipate a long-term issue, said despite the seven-wicket loss, England would take plenty of positives out of a series they won 2-1.
“We don’t take winning series for granted,” he added. “I think today was a kind reminder of how easily you can lose games when you have an average day or an off day.”