Nick Haining will now start at number eight, with Fagerson's Glasgow teammate Ryan Wilson - who could win his 50th cap - drafted in to join the replacements.
"Given Ryan's Test match experience and his form this season, we believe he will grab his opportunity," said head coach Gregor Townsend.
"Nick now has the opportunity from the start to show his abilities in what will be a great challenge for our forward pack. It's disappointing for Matt, who has been playing consistently well throughout the championship."
Edinburgh's Haining will be making his third international start and has come off the bench against Ireland and Italy in this season's tournament.