The hosts led 21-7 at the break and scored a fourth try early in the second half for a 28-7 score line, but the men in green and gold fought back from that deep hole and deserve credit for finishing strong.
It is clear that more time together on the training field will benefit the side in the next week when they face English Premiership side, Bristol Bears, as they started off with a stutter, but finished more composed in trying conditions against the Irish powerhouse team.
The first half started like a bang for the home side. Wing Shane Daly scored in the opening minutes when a slick Munster backline move proved too quick for the visiting backs to align to the decoy running of the home side. The A-side's midfield got cramped up and Daly had and easy run in from the space created by his inside backs.
Flyhalf Ben Healy, who just made the decisive pass to his wing, kicked a beauty from the corner and in a blink, Munster were 7-0 up.
It took the South Africans 10 minutes to finally fire a shot and it came via a couple of powerful scrums, which proved their best weapon of the night.
Fullback Aphelele Fassi kicked cleverly, forcing Munster to carry the ball over their own line, and then it was game on for the visitors. From there, a couple of dominant scrums by the SA 'A' side resulted in two consecutive scrum penalties.
Team captain Thomas du Toit opted for scrums every time and from the second of those, it was Fassi who went over in the right corner, with a good pass by Johan Goosen giving the fullback the space needed to score.
Goosen converted from a tight angle and the scores were even after 14 minutes.
The visiting scrum clearly had the upper hand early on, but the home side proved more cohesive in attack and general play during the next 20 minutes, which also saw the rain came down in Cork.
The lack of defensive coordination in the SA 'A' backline was again exposed soon after though. A Munster attack to the left, with some good decoy running, found the SA defence wanting and experienced wing Simon Zebo scored in the corner. Healy kicked a peach and suddenly the Irish were up 14-7 and gaining momentum in the game.
Ten minutes later, with the halftime oranges cut and ready to be served, two big plays occurred.
First, Munster had a very kickable opportunity to posts two minutes from time, but they opted for a lineout. That proved to be a great decision as they managed to get their maul going and the Munster pack drove over the line with Diarmuid Barron in possession.
Healy converted for a 21-7 lead and although the SA 'A' side had a scoring opportunity from the restart and actually twice opted for attacking lineouts, they lost the ball in a maul and it was a fine opportunity lost.
Munster started the second half with the same swagger. Healy stabbed through a grubber and fullback Mike Haley managed to get to it first and dotted down, with the confirmation from the TMO. Healy kicked the conversion and the lead grew to an alarming 28-7.
A couple of changes to the SA 'A' side saw Grant Williams coming off the bench and he immediately added some spark to the attack.
The next 15 minutes were all green and gold and Suleiman Hartzenberg was worked over in the corner 55 minutes in, but the DHL Stormers wing was ruled to have a foot in touch. Two minutes later, Sikhumbuzo Notshe was ruled to have dotted down just short of the line and from the resulting scrum, Munster were given a yellow card for repeated infringements.
True to core, Du Toit opted for yet another scrum, this time 5m out and against 14 men. The call proved to be a good one as Notshe's pick-and-go was decisive. Gianni Lombard, on for Goosen, converted to cut the lead to 14 points with just under 20 minutes to play.
The last 10 were frustrating for the visitors as they just could not get the next score needed to buckle Munster, but credit to the home side who managed to hang on against a SA 'A' side that showed a real hunger for the win, but sadly not the skill to do so.
Munster 28 (21) - Tries: Shane Daly, Diarmuid Barron, Simon Zebo, Mike Haley. Conversions: Ben Healy (4).
South Africa 'A' 14 (7) - Tries: Aphelele Fassi, Sikhumbuzo Notshe. Conversions: Johan Goosen, Gianni Lombard.