Sexton's calf injury, picked up on Leinster duty against Castres on 20 January, has not yet fully healed.
Munster flanker O'Mahony is out because of a hamstring problem, while Ulster wing Andrew Trimble is also a major doubt because of groin tightness.
"It's better to leave him [Sexton] out this weekend," Ireland's forwards coach Simon Easterby said.
"We don't want to compromise his calf any further."
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With 63-cap Sexton, 31, out of the Murrayfield contest, Ulster's Paddy Jackson looks certain to start in the fly-half jersey against the Scots.
Jackson started in Ireland's last game, the win over Australia in November, which was his 19th cap.
Munster fly-half Ian Keatley joined the squad as cover on Monday and appears likely to be on the bench at Murrayfield, with Bordeaux's Ian Madigan not in the squad for Saturday's match.
Keatley, 29, won the last of his four caps in the Six Nations game against Italy in Rome in 2015.
Uncapped Munster centre Rory Scannell could represent another fly-half option for Ireland coach Joe Schmidt.
Despite flanker O'Mahony's absence, Schmidt will still have strong back row options with fit-again Sean O'Brien, CJ Stander and Josh van der Flier all available to partner number eight Jamie Heaslip.
O'Brien, who has been out for a number of couple of weeks because of a calf injury, took a full part in training on Tuesday.
Trimble started in Ireland's Autumn Tests against New Zealand and Australia and his injury means that Keith Earls and Simon Zebo will be favourites to occupy the wing berths at Murrayfield, with Rob Kearney likely to remain at full-back.
Johnny Sexton and Peter O'Mahony will miss Ireland's Six Nations opener against Scotland on Saturday.