Murphy, who travelled as a backs reserve last weekend, comes straight into the starting team as does O'Mahony who was ruled out of the Edinburgh clash.
James Coughlan makes way for the province's returning skipper this Saturday and Donnacha Ryan shifts to blindside flanker where he replaces the injured Paddy Butler.
O'Callaghan resumes his second row partnership with O'Connell as Varley and Botha join David Kilcoyne in the front row. Cathal Sheridan takes the place of Duncan Williams on the bench.
Meanwhile, Category B Stand tickets (€40) and North/South Terrace tickets (€30) are still on sale for the Munster v Gloucester tie, with Category A tickets and East/West Terrace tickets sold out at this stage.
Tickets are on sale online here and are available from the Munster Rugby ticket offices in Thomond Park and Musgrave Park and Ticketmaster outlets nationwide, or by calling 0818 719300. Tickets will also be available to purchase on match day.
MUNSTER (v Gloucester): Felix Jones; Keith Earls, Casey Laulala, James Downey, Johne Murphy; Ian Keatley, Conor Murray; David Kilcoyne, Damien Varley, BJ Botha, Donncha O'Callaghan, Paul O'Connell, Donnacha Ryan, Niall Ronan, Peter O'Mahony (capt).
Replacements: Mike Sherry, James Cronin, Stephen Archer, James Coughlan, CJ Stander, Cathal Sheridan, JJ Hanrahan, Denis Hurley.