Munster will be the number one seeds in the Heineken Cup quarter-final draw after beating Northampton 51-36 at stadium:mk on Saturday.
Despite conceding two penalty tries, the two-time champions secured a bonus point to finish the pool stages with an unassailable 25 pool points.
The scores were locked at 19-19 at the break but winger Simon Zebo bagged a second-half hat-trick to help the Irish side maintain their perfect record of six wins from as many starts in Europe this season - the only team to do so.
The result, combined with the Scarlets' win over Castres, means that the Welsh side beat Saints to a place in the Amlin Challenge Cup quarter-finals.
Munster needed a win to ensure a quarter-final tie on home soil, but they got off to a poor start as they were bullied by a dominant Saints pack.
Ryan Lamb knocked over two early penalties and Northampton assumed control on 13 minutes when referee Roman Poite awarded them a penalty try as the visitors' scrum buckled under pressure.
However, the metronomic Ronan O'Gara kicked kept the scoreboard ticking with a series of three-pointers to narrow the gap before a Lamb drop-goal opened up a seven-point advantage.
Prop BJ Botha powered over from close range for the visitors before the opposing fly-halves traded penalties.
Munster started the second half furiously and tries from Johne Murphy and Zebo put them in charge at 31-19, although another penalty try bought Saints to within five points.
A resulting scuffle saw half-backs Lee Dickson and Connor Murray sin-binned.
O'Gara and Lamb then traded penalties before the visiting fly-half extended their lead with another three-pointer.
Zebo went over twice in the last 10 minutes, although Scott Armstrong scampered across the whitewash for a consolation score.
Tries: Penalty Try 2, Armstrong
Cons: Lamb 2, Myler
Pens: Lamb 3
Tries: Botha, Murphy, Zebo 3
Cons: O'Gara 3, Keatley
Pens: O'Gara 6
Yellow cards: Murray (Munster -59th min - handbags); Dickson (Northampton - 59th min - handbags)
Northampton Saints: 15 Ben Foden, 14 Jamie Elliott, 13 George Pisi, 12 James Downey, 11 Vasily Artemyev, 10 Ryan Lamb, 9 Lee Dickson, 8 Roger Wilson, 7 Phil Dowson, 6 Calum Clark, 5 Mark Sorenson, 4 Samu Manoa, 3 Brian Mujati, 2 Dylan Hartley (c), 1 Soane Tonga'uiha.
Replacements: 16 Brett Sharman, 17 Alex Waller, 18 Paul Doran Jones, 19 Christian Day, 20 Ben Nutley, 21 Martin Roberts, 22 Stephen Myler, 23 Scott Armstrong.
Munster: 15 Denis Hurley, 14 Johne Murphy, 13 Keith Earls, 12 Lifeimi Mafi, 11 Simon Zebo, 10 Ronan O'Gara, 9 Conor Murray, 8 James Coughlan, 7 Peter O'Mahony, 6 Donnacha Ryan, 5 Paul O'Connell, 4 Donncha O'Callaghan, 3 BJ Botha, 2 Damien Varley, 1 Wian du Preez.
Replacements: 16 Denis Fogarty, 17 Marcus Horan, 18 Stephen Archer, 19 Mick O'Driscoll, 20 Dave O'Callaghan, 21 Tomas O'Leary, 22 Ian Keatley, 23 Danny Barnes.
Venue: stadium:MK, Milton Keynes
Referee: Romain Poite (France)