Danny Wilson’s men went into the break with a slender 6-3 lead at BT Sport Cardiff Arms Park thanks to a pair of Steve Shingler penalties.
Aled Summerhill pounced for a decisive try while his side were reduced to 14-men and despite a Francis Saili try the Blues put up a herculean defensive effort.
Munster, with a strong wind at their backs, set up camp deep in Blues’ territory and took the lead in the closing stages thanks to a Rory Scannell drop-goal.
Cardiff Blues desperately rallied in the dying moments but Munster rubbed salt into the wounds as Conor Oliver broke through for a try to deny the home side a bonus point and put a major dent in the Blues' hopes of a top six finish.
The Blues made a solid start to the encounter with Nick Williams carrying to good effect off the back of an attacking scrum but Munster worked their way into the Blues half.
They had the first opportunity for point, following a high tackle in midfield, but pointed to the corner.
Wilson’s side defended the driving line-out superbly, sacking the Munster jumper and getting a drive on.
The Irish province managed to maintain possession and went through multiple phases but they were held at bay with Williams, clearly fired up to play one of his former teams, particularly prominent.
He made two thunderous hits in defence before namesake Lloyd Williams broke clear but play was called back for a penalty.
Keatley fired wide from the right touchline and the Blues cleared before working their way into the game.
Steve Shingler was narrowly off-target with a penalty from inside his own half but they remained in the ascendant.
Willis Halaholo displayed his attacking flair as he eased on the outside as he flicked a pass inside to release Tom James.
The wing broke play on an arcing run and found scrum-half Williams in support, but he was hauled down by Andrew Conway.
It appeared as though Munster had made two high tackles defending the next two phases but they were not penalised and were able to clear.
However James came back with another searing counter-attack on 20 minutes until he was brought crashing to earth by a well-timed Dave O’Callaghan hit.
Shingler finally broke the deadlock on 21 minutes, after George Earle was taken out in the air, but Rory Scannell equalised four minutes later.
Alarm bells were ringing after the Blues failed to secure a difficult high-ball under pressure and O’Callaghan broke clear. He was tackled short and the ball was spread wide but the Blues defended manfully and were eventually awarded a penalty for crossing.
Munster continued to look for opportunities on the counter-attack but it almost back-fired when Conway chipped over the top.
At full pace, Cardiff Blues captain Williams hacked the ball forward, on the volley. He won the footrace to collect but was tackled into touch in the corner.
However Munster were unable to exit and after a bout of handbags at the lineout the home side were awarded a penalty, which Shingler duly slotted from wide.
Rassie Erasmus’ side had the opportunity to respond after Josh Navidi was harshly penalised at the breakdown but Scannell pushed his straightforward penalty wide and the scores remained 6-3 at the interval.
Scannell was again off-target early in the second half but Munster were unfortunate not to score following an electric snipe from scrum-half Duncan Williams.
He raced 30 metres before being brought to a halt by Matthew Morgan and from the ensuing phase Munster knocked on.
However the Blues were dealt a major blow on 46 minutes when Halaholo was sin-binned for a high-tackle.
The Irish province sensed blood and kicked to the corner but they were penalised at the maul and Wales’ Capital Region cleared.
With the Blues’ back-line reduced to six-men, Munster looked to attack from wide but it back-fired when Navidi and Summerhill spot blitzed in defence with the wing pouncing for an interception.
Shingler converted to give his side an 11-3 advantage but the visitors quickly responded through Francis Saili.
He caught the Blues cold at the breakdown as he sniped through the middle to break clear and then wrong footed Matthew Morgan to score beneath the posts.
Scannell knocked over the extras to restore the three-point difference in scores and they almost gained a quick-fire second after a Scannell kick found space.
Conway won the footrace but knocked on in the process of grounding the ball, while it appeared he was also in touch.
With the advantage of a strong wind behind them, Munster dominated territory and possession. They were met by stern defence from the Blues, who time and time repelled them before working their way into the Irish half.
The home side were unfortunate not to receive a scrum after Conway knocked on in his own half before going on a counter-attack, which resulted in a penalty that Scannell converted.
After spending almost the entire half in Blues territory, Munster finally took the lead thanks to a Scannell drop goal.
With the clock ticking down, Conor Oliver dealt a further blow to the home side, as he raced away from a pick-up to touch down and deny a losing bonus point for Danny Wilson's side.