The reigning champions had Ronan O'Gara to thank for their place in the final four after the veteran fly-half kicked four penalties in the 13-12 defeat to Cardiff Blues.
A Jamie Roberts try had threatened to push the Blues into the semi-finals at the expense of Tony McGahan's men but the home side failed to record the eight-point margin of victory they required to jump into fourth spot ahead of the Leinster versus Edinburgh match.
A second-half injury time penalty from Leigh Halfpenny secured a seventh straight win in all competitions for the Blues, but it was Munster who left with the bigger prize. Munster will now face fellow Irish giants Leinster at the RDS on Saturday night (kick-off 8pm) in the second Play-Off semi-final.
Guinness PRO12
Suite 208, Alexandra House,
The Sweepstakes
Ballsbridge, Dublin 4, Ireland