Nick Robinson got things underway for the Blues with an early drop goal and try and American number eight Kort Schubert touched down twice.
Munster rallied when the home side had two men sin-binned in the second half. Their efforts were not enough. The Irishmen also lost influential Kiwi full-back Christian Cullen with a shoulder injury.
The Blues started well, piling on the pressure early and they were rewarded when Robinson dropped a superb left-footed goal. Munster soon drew level, with fly-half Paul Burke kicking a penalty after Blues acting captain Craig Quinnell was penalised at a ruck.
The Blues kept control, however, and a great break by full-back Nick Macleod put them in position to earn a short-range penalty.
They opted for a scrum and, when the ball was finally spun out, Robinson ducked inside a tackle to go over for a try. Lee Thomas converted and repeated the feat when Schubert pounced after charging down a clearance kick by Munster scrum-half Mike Prendergast.
A scissors move between Shaun Payne and Anthony Horgan sent the Irishmen into the home 22 for the first time and Burke put over a penalty to end the first half.
Thomas gave the Blues a flying start to the second period with another penalty, but Munster responded with a try for prop Horan following a driving line-out. Burke converted.
A last-ditch tackle by Thomas seemed to have saved the day for the Blues as Munster swept downfield, but Thomas was penalised for not rolling away and Scottish referee Mike Hall pulled out the yellow card.
But the Blues survived some frantic exchanges on their own line before taking play to the other end, where Schubert caught a line-out throw and dived over. In the absence of Thomas, Macleod added the extras.
Munster hit back again and Blues flanker Robin Sowden-Taylor became the second player to visit the sin bin. Hardly had he left the field than Munster hooker Frankie Sheahan forced his way over and Burke's kick cut the gap to seven points.
But it was the Blues who grabbed the only other points with Thomas slotting over a final penalty.
FINAL SCORE: BLUES 30-20 MUNSTER
Blues: (17) 30: Tries: N Robinson, Schubert 2. Cons: L Thomas 2, MacLeod. Pens: L Thomas 2. DG: N Robinson.
Munster: (6) 20: Tries: Horan, Sheehan. Cons: Burke 2. Pens: Burke 2.
N Macleod; D Dewdney, T Davies, L Thomas, C Morgan; N Robinson, R Powell; M Jones, G Williams, B Evans, C Quinnell (capt), D Jones, M Molitika, R Sowden-Taylor, K Schubert.
Replacements: J Vaughton, D Hewitt, R Smith, N Llewellyn, R Thomas, J Goode, N Thomas.
C Cullen; J Kelly, S Payne, R Henderson, A Horgan; P Burke, M Prendergast; M Horan, F Sheahan, G McIlwham, T Bowman, T Hogan, J Williams, D Wallace, S Keogh.
Replacements: F Roche, J Flannery, T Hayes, A Quinlan, E Reddan, J Holland, P Devlin.