Peter O'Mahony will now move from the replacements to start at number 7, with Shane Jennings being called into the squad to take O'Mahony's place on the bench.
Ireland team manager Michael Kearney said: "We knew Sean was carrying this infection in his foot, but unfortunately it has not cleared as quickly as we expected.
"While it has not healed enough for him to play this Saturday, we expect him to be fine for next weekend.
"With Sean out, we have decided to bring Peter into the starting side and Shane Jennings into the squad."
IRELAND Team & Replacements (v Scotland, 2012 RBS 6 Nations Championship, Aviva Stadium, Saturday, March 10, kick-off 5pm):
15 - Rob Kearney (UCD/Leinster)
14 - Tommy Bowe (Ospreys)
13 - Keith Earls (Young Munster/Munster)
12 - Gordon D'Arcy (Lansdowne/Leinster)
11 - Andrew Trimble (Ballymena/Ulster)
10 - Jonathan Sexton (St. Mary's College/Leinster)
9 - Eoin Reddan (Lansdowne/Leinster)
1 - Cian Healy (Clontarf/Leinster)
2 - Rory Best (Banbridge/Ulster) (capt)
3 - Mike Ross (Clontarf/Leinster)
4 - Donncha O'Callaghan (Cork Constitution/Munster)
5 - Donnacha Ryan (Shannon/Munster)
6 - Stephen Ferris (Dungannon/Ulster)
7 - Peter O'Mahony (Cork Constitution/Munster)
8 - Jamie Heaslip (Naas/Leinster)
16 - Sean Cronin (St. Mary's College/Leinster)
17 - Tom Court (Malone/Ulster)
18 - Mike McCarthy (Buccaneers/Connacht)
19 - Shane Jennings (St. Mary's College/Leinster)
20 - Tomas O'Leary (Dolphin/Munster)
21 - Ronan O'Gara (Cork Constitution/Munster)
22 - Fergus McFadden (Old Belvedere/Leinster)