It was a tale of two kickers in the first half as Rhys Patchell booted Blues into the lead before JJ Hanrahan brought the teams level at 9-9 after a tight and evenly contested opening 40 minutes.
Home captain Denis Hurley scored to put Munster ahead at the start of the second period before a clinical team effort saw Number Eight Jack O’Donoghue dot down to open up the lead.
In-form back row Josh Navidi picked up and crashed over to give Blues late hope as temperatures tumbled in Cork.
But the final word went to Munster as wing Ronan O’Mahony scored in the final few seconds as Blues left Ireland empty-handed.
The early pressure in the game came from the hosts and a penalty at the breakdown gave Hanrahan the chance to opening the scoring on ten minutes.
The full back, who took over kicking duties with Ian Keatley a late home withdrawal with illness, hit the left post with his first effort but another penalty was awarded just moments later and this time he split the uprights for the lead.
Joaquin Tuculet and Manoa Vosawai combined from deep to give the visitors front foot ball in response. And some slick handling from Gavin Evans and Richard Smith forced Munster back before a penalty allowed Patchell to take aim and bring the sides level.
Welsh ace Allen was looking a threat with ball in hand as he danced past two tacklers with ease while Patchell looked to play for territory as he kicked in behind Munster.
Smith showed his raw pace with an electric break down the right flank and another penalty, this time for not releasing against the home side, was again nudged over by Patchell for the lead.
Alert play from scrum half Lloyd Williams saw him kick in behind into space, after Tuculet soared highest to claim a high kick, before a driving maul drove Munster back before Williams spilled under pressure as he looked to peel off the back.
Josh Turnbull carried powerfully before more decisive work at the breakdown from the visiting forwards secured a penalty and Patchell did the rest for a 9-3 lead after half an hour.
Blues were then forced into a front row reshuffle, with Thomas Davies and Kristian Dacey introduced before half-time for Sam Hobbs and Matthew Rees, and two quick-fire penalties from Hanrahan leveled the teams up at the break.
Mark Hammett’s men looked wide at the start of the second half with Evans and Tuculet striving to exploit gaps.
A stolen lineout, though, and then a subsequent penalty for not releasing allowed Munster to finally claim some territory in the second half and they made it count in decisive fashion.
O'Donoghue made a powerful break to start the attack, O'Mahony showed nice footwork and only a superb tackle stopped Hanrahan from scoring close to the line. But there was no stopping Hurley who picked up and burrowed over from close range.
The home side were ominously beginning to click up the gears and dominate territory and possession, with Blues left with scraps to work with as they started to use the replacements bench to try and turn the growing tide.
Tom Isaacs, back from injury, was straight into his defensive duties with two big tackles, but the home side were happy to play in the visiting half and force Blues to try and create from deep.
A second home try looked inevitable, such was the territory, and arrived on the hour when Hurley broke away from deep inside his own 22 and fed the marauding Keith Earls who brushed off several tackles.
With players scattered across the field, the ball was quickly fed down the line left and O’Donoghue raced through a hole to score to a huge ovation.
Munster were looking threatening with every attack and only a booming clearing kick from Allen forced them back, with Smith giving chase to force the turnover.
However, from nowhere Argentine duo Tuculet and Amorosino sparked into life down the left wing and replacement Ellis Jenkins thundered into contact and punched a big gap in the Munster defence.
Suddenly Blues were on the front foot and hooker Dacey kept momentum going, as he made gains down the middle, before Navidi picked up and, despite the attention of several tacklers, rolled out and crashed over to give Blues hope.
Hopes of a comeback, though, were short-lived as a testing high up and under kick from Hanrahan was brilliantly plucked from the night sky by Darren Sweetnam who set off for the try line.
The hard-working Allen hauled him down but moments later a penalty for not releasing gave Hanrahan the simplest of kicks from in front to put Munster ten points ahead.
And it was the hosts who had the final say when, after several phases down the left, O’Mahoney spotted a gap on the right as play was switched and raced to the corner to score.
11m Hanrahan p 3-0
14m Patchell p 3-3
18m Patchell p 3-6
30m Patchell p 3-9
35m Hanrahan p 6-9
39m Hanrahan p 9-9
48m Hurley t Hanrahan c 16-9
60m O’Donoghue t Hanrahan c 23-9
70m Navidi t Patchell c 23-16
77m Hanrahan p 26-16
80m O’Mahony t Hanrahan c 33-16
Cardiff Blues: 15 Joaquin Tuculet, 14 Richard Smith, 13 Cory Allen, 12 Gavin Evans (Isaacs 55), 11 Lucas Amorosino, 10 Rhys Patchell, 9 Lloyd Williams (Knoyle 58); 1 Sam Hobbs (Davies 29-40, 50), 2 Matthew Rees (Dacey 31), 3 Adam Jones (Filise 55), 4 Macauley Cook, 5 Filo Paulo, 6 Josh Turnbull, 7 Josh Navidi, 8 Manoa Vosawai (Jenkins 63)
Replacements: 16 Kristian Dacey, 17 Thomas Davies, 18 Taufa’ao Filise, 19 Miles Normandale, 20 Ellis Jenkins, 21 Tavis Knoyle, 22 Gareth Davies, 23 Tom Isaacs