The Cardiff Blues snatched a fine 13-12 win over on Sunday, but it wasn't enough to see them through to Magners League play-offs.
Munster, for their part, will do battle with Leinster in Dublin for a place in the final.
A massive penalty from inside his own half by Leigh Halfpenny gave the Blues the dramatic victory in injury time - only for Munster to progress thanks to their losing bonus point.
As news of an Edinburgh lead in Dublin filtered through, it had seemed as if neither side was going to qualify from the Cardiff City Stadium, but Leinster's late tries helped their countrymen make the last four.
Nerves played a part early on, with passes going astray on both sides and Blues fullback Ben Blair did little to ease the tension among the 12,602 crowd by missing two long-range but kickable penalties.
He finally broke the deadlock with a simple effort from in front of the post, but within two minutes Ronan O'Gara had levelled when the Blues' backs strayed offside.
Two pinpoint kicks for position by the Ireland fly-half forced the Blues to concede a scrum five, but a Martyn Williams' tackle held Munster number eight David Wallace up just short of the line.
The Blues, showing commendable adventure with limited possession, ran a penalty from deep and the attack culminated in centre Jamie Roberts forcing his way over despite the attentions of three Munster defenders, Blair converted from wide out, but O'Gara's boot dominated the remainder of the half, with a trio of penalties edging Munster in front by the interval.
The Irish province tried to raise the tempo in the second half, pinning the Blues in their own 22, but were rocked when prop Marcus Horan was yellow-carded for slowing down home ball.
A break by Maama Molitika, carried on by Ceri Sweeney, raised Blues hopes of a second try, but Munster swept back downfield and wing Tom Gleeson came close from another inch perfect kick by O'Gara.
Munster's acting captain missed a shot at goal for the first time, however, but showed his ability with ball in hand when he jinked through a static defence, only for his tri-scoring pass to Jean de Villiers to be controversially judged forward.
At the other end, replacement number eight James Coughlan had to be quick to reach a Martyn Williams pass ahead of Blues substitute Dafydd Hewitt.
Halfpenny's huge penalty proved the only score of the second period raising a deafening cheer from the Blues' supporters but failing to prevent Munster moving on to the next stage of the competition.
For Cardiff Blues:
Pens: Blair, Halfpenny
Pens: O'Gara 4
Yellow card(s): Horan (Munster), 52.
Cardiff Blues: 15 Ben Blair, 14 Leigh Halfpenny, 13 Casey Laulala, 12 Jamie Roberts, 11 Chris Czekaj, 10 Ceri Sweeney, 9 Darren Allinson, 8 Xavier Rush, 7 Martyn Williams, 6 Maama Molitika, 5 Paul Tito (capt), 4 Deiniol Jones, 3 Scott Andrews, 2 T Rhys Thomas, 1 Gethin Jenkins.
Replacements: 16 Gareth Williams, 17 John Yapp, 18 Bradley Davies, 19 Sam Warburton, 20 Lloyd Williams, 21 Dai Flanagan, 22 Dafydd Hewitt.
Munster: 15 Scott Deasy, 14 Denis Hurley, 13 Keith Earls, 12 Jean de Villiers, 11 Lifeimi Mafi, 10 Ronan O'Gara (capt), 9 Peter Stringer, 8 David Wallace, 7 Niall Ronan, 6 Nick Williams, 5 Billy Holland, 4 Donncha O'Callaghan, 3 Tony Buckley, 2 Damien Varley, 1 Marcus Horan.
Replacements: 16 Mike Sherry, 17 Dave Ryan, 18 Alan Quinlan, 19 James Coughlan, 20 Tomas O'Leary, 21 Paul Warwick, 22 Danny Barnes.
Referee: Peter Allan (SRU)
Assistant Referees: Hugh Watkins (WRU), Simon Harris (WRU)
TMO: Tony Rowlands (WRU)