And Morgan insisted he would have "no worries" about Bairstow opening – something he has yet to do in international cricket. Morgan would not confirm his XI at Tuesday's pre-match press conference in Cardiff but said there was "a chance we could make a change".
Surrey opener Roy has averaged just 6.37 from eight ODI innings this season, with a mere two double-figure scores. Morgan had been staunch in his support of Roy before the Champions Trophy started, saying: "The decision remains the same throughout the tournament...he'll definitely play."
However, that backing has softened in the light of Roy's repeated failures and Morgan, fresh from his impressive 87 in England's group win over Australia, indicated Tuesday the team could not afford to 'carry' anyone as they went in search of a first major ODI tournament triumph.
"I mentioned after the last game that we're getting to the business end of the tournament and we need to produce results, so it's important that we get what we feel is our best XI to win the tournament out tomorrow (Wednesday) in order to win the game," said Morgan.
Bairstow, in marked contrast to Roy, has scored three fifties in his last four ODI innings when standing in for others in England's top order.
Although he's yet to open in ODI cricket, Test wicket-keeper Bairstow's highest List A score of 174, for Yorkshire against Durham last month, at the top of the order.
"Jonny's qualities are that he's a fantastic batsman," Morgan said.
"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 cited Bairstow's unbeaten 83 in England's ODI series-clinching win over New Zealand at Chester-le-Street in 2015 as proof of the 27-year-old's ability to rise to the occasion.
"One innings he did play for us won us a series, against New Zealand, a match-winning knock up at Durham two years ago sums him up," Middlesex left-hander Morgan said.
"He came from playing for Yorkshire, straight into the squad having played no part in the series, and he produces a match-winning knock. So I think his all-round ability is as good as we have in the squad.
"But, like I've mentioned before, it's a very difficult team to get into and you've just got to wait for your chance," he added.
"I'd have no worries if he has to open the batting...If Jonny does get the opportunity, I'm sure he'll take it with both hands."
Pakistan coach Mickey Arthur said he would be glad if Roy was left out.
"I was particularly worried that Roy hadn't fired yet because I think he's very close to something quite good," said Arthur. "So if he's not playing, that wouldn't be too bad."
But the South African, who denied using "mind games", was well aware of Bairstow's quality, having seen him score an unbeaten 61 on his Headingley home ground in a four-wicket ODI victory against Pakistan last year.
Bairstow was only called into the England side shortly before the start after Jos Buttler suffered a hamstring injury in the warm-up.
"He wasn't supposed to play half an hour before the game, got roped in for Buttler, and got man-of-the-match, recalled Arthur.
"So that was an incredible performance.
"The only thing I will say, I know that Bairstow has opened at county level, he's never done it internationally, and I think that's a different ball game."