The tourists made one further change, replacing seam-bowling all-rounder Fahim Ashraf with leg-spinner Shadab Khan on a used pitch.
Bairstow impressed for England during a short series against Ireland prior to the start of the Champions Trophy, and while there were calls for his inclusion during the three-match rubber against South Africa, Morgan and Trevor Bayliss chose to back Roy instead.
As the nation was busy in praising and celebrating its cricket team's splendid victories one after another, former Pakistan opener Aamer Sohail on Thursday indirectly alleged that the other team deliberately threw matches in Pakistan's favor in the ongoing Champions Trophy.
Sarfraz Ahmed, Pakistan's captain, is hoping that Hasan will shine again in Sunday's final at The Oval.
England collapsed to 211 all out, with no batsman making a fifty in an innings where they could not manage a single six.
Meanwhile Michael Vaughan, another ex-England captain, said in his Daily Telegraph column that he felt "flatter" than at the time of their World Cup exit two years ago.
"This was a golden chance to win a tournament at home, and I think all we can do now is keep looking towards that World Cup and use this as a really good platform".
London fire could delay deal between UK PM May's Conservatives and DUP
Talks with the DUP to secure her government broke up on Tuesday night without an agreement, but Mrs May said the discussions had been "productive".
"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".
"Jonny is a fantastic batsman and I think his best attribute, certainly in white ball cricket over the last year-and-a-half, has been his relentless attitude to score runs regardless of the situation", Morgan said.
"We've played worse than this over the last couple of years and been knocked over fairly easily in some games, (but) it doesn't seem to affect them", he said.
'We were disappointed not to beat Pakistan because we had been playing well enough but we still have a bit of work to do.
"Their coach Trevor Bayliss has always asked for them to play smart cricket, not just gung-ho cricket". There's a number of our guys who haven't been at this level before and it is a learning curve.
"Coming from Edgbaston which was a good wicket to a used wicket, we didn´t adapt very well", Morgan told Sky Sports.