All return to play protocol has been followed and the Munster skipper has progressed normally in this regard.
However, due to the heavy schedule in the upcoming weeks, including RaboDirect PRO12, Heineken Cup and possible International involvement, a decision to omit him from this weekend's opening Heineken Cup game against Edinburgh has been made.
In the flanker's absence, Paul O'Connell will captain the province when they run out in Murrayfield on Saturday afternoon.
With O'Mahony ruled out, there is one change to the pack that defeated Leinster with Paddy Butler coming into the side to make his first Heineken Cup start, as he joins Niall Ronan and James Coughlan in the back row.
There is one change to the backline also with Conor Murray making his first start of the season at scrum half, with Duncan Williams named on the replacements bench.
MUNSTER (v Edinburgh): Felix Jones; Keith Earls, Casey Laulala, James Downey, Simon Zebo; Ian Keatley, Conor Murray; David Kilcoyne, Mike Sherry, Stephen Archer, Donnacha Ryan, Paul O'Connell (capt), Paddy Butler, Niall Ronan, James Coughlan.
Replacements: Damien Varley, James Cronin, BJ Botha, Donncha O'Callaghan, CJ Stander, Duncan Williams, JJ Hanrahan, Denis Hurley.