Centre-back Duffy, 20, was recalled by the Premier League side on Thursday as a result of Jagielka's injury.
Everton have confirmed he will be out for around a month-and-a-half due to medial ligament damage in a knee.
Duffy is likely to be thrust into the matchday squad to face non-league side Tamworth in the FA Cup third round on Saturday, with a place in the starting line-up not unlikely given his experience against lower league opposition this season.
He is not Cup-tied as he was left out of Scunthorpe's games in the competition earlier in the campaign.
The Iron said they hoped to secure Duffy's return on loan ahead of next week's League One game at Cheltenham, but it is unlikely Everton manager David Moyes would allow him to leave the club until either Jagielka is back at full fitness or he has signed another defender.
"It's disappointing for us to lose Shane but there's a chance we may have him back. He's gone back as cover," Alan Knill, the Iron manager,told the official Scunthorpe United website.
"I've spoken to David Moyes and he couldn't really do anything about it, but he's on a youth loan so they can always go back and play for their club and then come back on loan after that. We are hopeful but we'll just have to wait."