O'Connell, who is nursing a bad back, sat out training in Limerick on Thursday morning and on Friday it was decided to omit him for the trip to Wales.
Munster team manager Shaun Payne said: "It's nothing serious, Paul has a busy summer ahead of him and we felt it just wasn't in his best interests to play this weekend.
"However, we would be confident he will be involved in the final game of the season against the Ospreys next week."
Munster include 13 players who were involved last weekend at Croke Park for a game that this time last week was seen as a potential dry run for the Heineken Cup final until the intervention of Leinster and the Leicester Tigers.
Also included in the starting line-up for the Arms Park encounter is Brian Carney on the right wing and Jeremy Manning at out-half.
There is an all-Limerick centre partnership in Barry Murphy and Keith Earls, with Lifeimi Mafi ruled out due to suspension.
Up front Nick Williams takes over from Alan Quinlan in the back row, where Niall Ronan is also in in place of David Wallace.
Munster Academy players, Dave Foley from UL Bohemians and Conor Murray from Garryowen, could make their senior debuts for the province off the bench.
Meanwhile, Cardiff coach David Young has named four 2009 Lions squad members in his side for Sunday's encounter.
Young has insisted he will continue playing his Lions players until automatic Heineken Cup qualification is secured, despite the injury to Tom Shanklin in the last match against the Dragons that saw his Lions dream shattered.
Leigh Halfpenny starts at full-back, while Jamie Roberts, Andy Powell and Martyn Williams all figure in the starting line-up.
The Blues' remaining Lion, Gethin Jenkins, is being rested for this game.
CARDIFF BLUES: Leigh Halfpenny; Richard Mustoe, Jamie Robinson, Jamie Roberts, Chris Czekaj; Nicky Robinson, Darren Allinson; John Yapp, Gareth Williams, Gary Powell, Bradley Davies, Scott Morgan, Sam Warburton, Martyn Williams, Andy Powell.
Replacements: Sam Hobbs, Rhys Thomas, Deiniol Jones, Ben White, Richie Rees, Ceri Sweeney, Tom James.
MUNSTER: Denis Hurley; Brian Carney, Barry Murphy, Keith Earls, Ian Dowling; Jeremy Manning, Peter Stringer; Federico Pucciariello, Denis Fogarty, John Hayes, Donncha O'Callaghan, Mick O'Driscoll (capt), Nick Williams, Niall Ronan, Denis Leamy.
Replacements: Mike Essex, Tony Buckley, James Coughlan, Dave Foley, Conor Murray, Paul Warwick, Kieran Lewis.
Referee: Peter Allan (Scotland)
Assistant Referees: Gwyn Morris, Leighton Hodges (both Wales)
Television Match Official: Neil Ballard (Wales)
Match Odds (Paddy Power): Cardiff Blues to win: 8/13; Draw: 20/1; Munster to win: 13/10
Say What: David Young (Cardiff Blues) - "I would like to offer my congratulations to Munster on winning the Magners League.
"The manner in which they won it this season shows that they are a quality outfit and have strength throughout their squad.
"We have seen their quality in the Heineken Cup over recent seasons and it is no surprise to me that they performed so well in the league this year.
"Like ourselves, they have a handful of Lions and were knocked out of the Heineken Cup in the semi-final stage.
"Whatever team they field, I am sure that we will have to be at our best to get the win."
Top Scorers: 2008/09 Magners League - Points: Cardiff Blues: Ben Blair 84; Munster: Paul Warwick 83; Tries: Cardiff Blues: Leigh Halfpenny, Ma'ama Molitika, Ceri Sweeney, Jamie Robinson 3 each; Munster: Keith Earls 8
RECENT LEAGUE MEETINGS:
Saturday, May 27, 2006 - Munster 37 Cardiff Blues 8, Thomond Park
Friday, September 1, 2006 - Cardiff Blues 22 Munster 13, Arms Park
Friday, March 2, 2007 - Munster 12 Cardiff Blues 19, Musgrave Park
Friday, October 5, 2007 - Munster 19 Cardiff Blues 17, Musgrave Park
Saturday, March 1, 2008 - Cardiff Blues 25 Munster 22, Arms Park
Saturday, September 20, 2008 - Munster 28 Cardiff Blues 20, Musgrave Park
- Cardiff Blues hosted the Newport Gwent Dragons last Wednesday, scoring a 26-12 victory. The Welshmen have won three of their last four games against Irish opponents, whilst the last Irish side to win at the Arms Park was Leinster (30-19) in the Magners League on September 28, 2007
- Munster became Magners League champions last week when the Ospreys were unable to secure a maximum-point win over the Dragons. This represents the earliest date the title has been decided since the advent of home and away league rugby in the 2003/04 season
- The Munstermen have won their last seven matches in the Magners League - their best run since the 2004/05 campaign
- Munster have won their last nine games against Welsh opponents since their most recent visit to the Arms Park in March 2008