Northampton's Ben Foden beats Ronan O'Gara to the high ball
Munster secured a home quarter-final in the Heineken Cup with this battling win while Northampton could also progress after earning a bonus point.
Ronan O'Gara kicked two first-half penalties for Munster, while Bruce Reihana converted a Saints penalty to leave it 6-3 at the break.
Shane Geragthy levelled with a penalty, only for O'Gara to put Munster six clear with two more penalties.
Stephen Myler's late penalty proved to be in vain for the English visitors.
Munster were forced into a change just before kick-off with Ian Dowling coming in for the injured Denis Hurley on the left wing.
The hosts, spurred on by a vociferous Thomond Park crowd, made a strong start and O'Gara fired over the opening penalty after three minutes.
Northampton gradually worked their way into a tight and tense contest which became bogged down in the middle third.
Saints fly-half Geraghty sliced a long-range drop-kick wide before O'Gara saw his penalty drop short of the post.
Reihana levelled for the visitors with a finely struck penalty in the 32nd minute.
O'Gara won a penalty after breaking through the Northampton line on the stroke of half-time and he slotted over to put the Irishmen in front.
The Saints pressed on the restart but first Reihana and then Geraghty wasted penalty chances.
Geragthy finally brought the visitors level on 53 minutes with a penalty in front of the posts, only for O'Gara to restore Munster's lead with a penalty four minutes later.
Northampton squandered a rare sniff of a try when Dylan Hartley was held up just short of the line after he charged down a Tomas O'Leary clearance.
The visitors failed to get over from two scrums as they pinned Munster back although Paul O'Connell was sinbinned for hands in a ruck.
Munster took inspiration from their escape and O'Gara increased the gap to six points with a penalty nine minutes from time.
Replacement Myler set up a thrilling finish after a 76th minute penalty but that was the final score of the game.
Munster top Pool One on 24 points with Northampton back on 19 and hoping to go through as one of the best runners-up.
Munster captain Paul O'Connell
"We knew it was going to be an unbelievably tough game - Northampton are a team with a lot of confidence.
"We are very happy to win here. We didn't play fabulously well but we dug deep and produced the result."
Northampton director of rugby Jim Mallinder
"We did play well although some of our decision making wasn't always very good at times.
"We were getting on top in the second half. We had a series of scrums and they had 14 men - that was a real missed opportunity.
"We missed a couple (of penalties) and when you come to places like this you have to take your chances."
Munster: Paul Warwick, Doug Howlett, Keith Earls, Jean de Villiers, Ian Dowling, Ronan O'Gara, Tomas O'Leary, Wian de Preez, Denis Fogarty, John Hayes, Donnacha O'Callaghan, Paul O'Connell (capt), Alan Quinlan, Niall Ronan, David Wallace. Replacements: Horan for du Preez (68), Varley for Fogarty (56), Buckley for Hayes (72), D Ryan for O'Callaghan (56). Not Used: Coughlan, Stringer, Mafi, Gleeson.
Sin Bin: O'Connell (62).
Northampton: Ben Foden, Chris Ashton, Jon Clarke, James Downey, Bruce Reihana, Shane Geraghty, Lee Dickson, Soane Tonga'uiha, Dylan Hartley (capt), Euan Murray, Ignacio Fernandez Lobbe, Juandre Kruger, Courtney Lawes, Phil Dowson, Roger Wilson. Replacements: Myler for Geraghty (73), Day for Fernandez Lobbe (59), Best for Lawes (73). Not Used: Sharman, Waller, Mujati, Dickens, Mayor.
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