With a number of injuries to Ulster's senior squad ahead of a huge Challenge Cup Semi-Final against Exeter Chiefs, Richie Murphy rang the changes, with five Academy players playing on the night.
There were senior Ulster debuts for Academy trio James McKillop, Tom Brigg and Aitzol Arenzana-King, while tighthead prop Bryan O'Connor made his first senior start for the province.
Michael Lowry captained the side for the first time in a competitive match.
Facing a full-strength Munster side in Limerick, Murphy's young side started off with intensity and front footed rugby.
After early territory in Munster's 22, James McKillop found a gap in the Munster rearguard and drove towards the line. His effort was short but as he was dragged over the tryline, he was adjudged to have been held up by the referee.
Ulster felt confident in the early stages, helped by a strong set piece. At one point a break looked on, but for Calvin Nash's knock forward resulting in a scrum penalty.
Ulster kept playing into space and worked it out wide, with Michael Lowry taking heavy contact and releasing a pass out to Aitzol Arenzana-King, who produced a spectacular finish in the corner for a debut try.
Munster regrouped and went on the attack, forcing Ulster into an unfortunate error, as debutant flanker Tom Brigg was shown a yellow card for what was adjudged to be a deliberate knock on.
With Ulster a man down, Munster punished the visitors with John Hodnett scoring two tries during that period.
The first on 24 minutes came from a lineout maul, with the flanker peeling off and the second on the 29th minute was another close range drive over the line. With Hanrahan's successful conversion, the scoreline was 12-7.
Ulster also had to deal with multiple injury setbacks, with Ben Carson coming off for Jonny Scott, while Eric O'Sullivan and Bryan O'Connor were replaced by Callum Reid and Tom McAllister respectively.
At the break, Munster led by five points.
HT: Munster Rugby 12-7 Ulster Rugby
Munster came out for the second half and were forced into an early change with Tom Farrell coming off for Alex Kendellan.
Kendellan's impact was immediate, as the replacement scored the third try on the 48th minute, producing a finish after a strong carry and break from Tom Ahern.
Kendellan would add his second in the 53rd minute, collecting Craig Casey's pass to finish under the posts for the hosts' bonus point fourth try.
John Hodnett would score a hat trick third try in the 56th minute, after sharp play from Casey and Coombes setting the flanker up on the wing for the score.
With Ulster having five Academy players on the field, the team kept carrying hard and kept trying to force their way into Munster territory.
That spirit showed when replacement hooker, John Andrew, was able to power his way over from an attacking lineout to score Ulster's second try of the match in the 66th minute. Jake Flannery adding the conversion.
Munster would reply just two minutes later, with John Hodnett being found on the left wing this time by Dan Kelly and the flanker had the power to break the covering tackle and score his fourth of the match.
In the 70th minute, with Ulster working the ball in an attacking phase within the Munster half, a loose pass was punted down the field from Kendellan, who then found himself in a length of the field foot race with replacement fly-half, James Humphreys.
Despite Humphreys' admirable attempts to ground the ball and prevent Kendellan over the line, a TMO check confirmed that the Munster man had done enough to get the contact and register his third of the match.
Ulster pressed in the closing stages, but were ground out by the home side who took the five points.
The province could be proud of the efforts of their young talent and changed side, who played some excellent rugby in the opening half before Munster's strong second half performance.
Richie Murphy's side now look ahead to a Challenge Cup semi-final against Exeter Chiefs at Affidea Stadium next Saturday before their attentions return to URC action in two weeks time.
FT: Munster Rugby 41-14 Ulster Rugby
A proud day for the Academy
Scorers
Munster Rugby:
TRY: Hodnett (4), Kendellan (3)
CON: Hanrahan (3)
Ulster Rugby:
TRY: Arenzana-King, Andrew
CON: Flannery (2)
Teams
Munster Rugby:
15. Shane Daly; 14. Calvin Nash, 13. Tom Farrell, 12. Alex Nankivell, 11. Andrew Smith; 10. JJ Hanrahan, 9. Craig Casey, 8. Gavin Coombes, 7. John Hodnett, 6. Tom Ahern, 5. Tadhg Beirne (capt), 4. Jean Kleyn, 3. Oli Jager, 2. Diarmuid Barron, 1. Jeremy Loughman
Replacements: 16. Lee Barron, 17. Michael Milne, 18. Michael Ala’alatoa, 19. Edwin Edogbo, 20. Brian Gleeson, 21. Ben O’Donovan, 22. Dan Kelly, 23. Alex Kendellen.
Ulster Rugby:
1. Eric O’Sullivan, 2. James McCormick, 3. Bryan O’Connor, 4. Harry Sheridan, 5. Charlie Irvine, 6. James McKillop, 7. Tom Brigg, 8. Lorcan McLoughlin, 9. Conor McKee, 10. Jake Flannery, 11. Ben Moxham, 12. Ben Carson, 13. Ethan McIlroy, 14. Aitzol Arenzana-King, 15. Michael Lowry (C)
Replacements: 16. John Andrew, 17. Callum Reid, 18. Tom McAllister, 19. Joe Hopes, 20. Marcus Rea, 21. David Shanahan, 22. James Humphreys, 23. Jonny Scott