However, having successfully followed a modified training schedule this week, the talismanic Ireland flanker is included in Rob Penney's starting line-up to face the French giants.
The only other change to the side sees James Downey renew his centre partnership with Casey Laulala.
With O'Mahony back to lead the team, South African CJ Stander reverts to the replacements bench.
Meanwhile, reserve prop John Ryan takes the place of James Cronin who is ruled out with an ankle sprain.
Alan Cotter and Gerhard van den Heever, who was added to the province's European panel last month, are both named in their first Heineken Cup matchday squad.
MUNSTER (v Toulouse): Felix Jones; Keith Earls, Casey Laulala, James Downey, Simon Zebo; Ian Keatley, Conor Murray; David Kilcoyne, Damien Varley, BJ Botha, David Foley, Paul O'Connell; Peter O'Mahony (capt), Tommy O'Donnell, James Coughlan.
Replacements: Duncan Casey, John Ryan, Alan Cotter, Donncha O'Callaghan, CJ Stander, Duncan Williams, JJ Hanrahan, Gerhard van den Heever.