He has now been ruled out of Saturday's RaboDirect PRO12 clash with Glasgow Warriors and the remainder of the season after undergoing surgery to reconstruct his shoulder.
With four matches left of the regular league season, Munster are currently placed second in the table five points behind Irish rivals Leinster.
And Munster said in a statement: "Peter O'Mahony is to undergo reconstructive shoulder surgery this morning and is ruled out for the remainder of the season.
"O'Mahony travelled to Dublin late yesterday evening for a review with the specialist, and following the consultation it was confirmed that the Munster captain required surgery on his left shoulder.
"Peter sustained the injury in the opening 20 minutes of Munster's 47-23 victory against Toulouse on Saturday after he over-extended his shoulder."
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Guinness PRO12 Munster News
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