Fly-half Ian Keatley got Munster off to the perfect start with a penalty after just two minutes as rain made running rugby difficult for both sides.
It took nearly 20 minutes for a much-changed Ulster outfit to make their first incursion into the Munster 22, but Niall O'Connor was able to level the scores with the boot as he knocked over his second penalty attempt to make it 3-3.
Munster were in the ascendancy, however, and with half an hour gone they forced a series of scrums on the Ulster five-metre line, with referee Alain Rolland blowing for a penalty try that Keatley converted to give his side a 10-3 lead.
Six minutes before the break Ulster scrum-half Paul Marshall was shown the yellow card for infringing at the ruck and although they made it to half-time without conceding any further points, his absence was to prove crucial.
With Marshall still off the field Munster winger Simon Zebo came off his flank and broke through a huge gap in midfield to touch down unchallenged near the posts.
Keatley added the extras and at 17-3 Ulster were staring defeat in the face, and their task wasn't made any easier on 49 minutes when Munster added their third try of the game.
With Ulster forced deeper and deeper into their 22, Irish international back row Peter O'Mahony powered over from close range to put the result out of doubt. Keatley's unerring boot made short work of the conversion and with the scoreline 24-3 it led to both sides ringing the changes.
Despite their best efforts Ulster were unable to force their way back into the game until the final minute when replacement Alistair Birch grabbed his first senior try for the club.
The 24-year-old back row finished off a scintillating Ulster move that saw the visitors break down the right where the restored Marshall flicked the ball inside to Robbie Diack whose pass found Birch on his shoulder to dive over the line.
Replacement Stuart Olding added the extras to give the scoreline a respectable feel, but league leaders Ulster finally gave up their 100 per cent record in this year's RaboDirect PRO12.
|Munster Rugby Score Card|
|Ulster Rugby Score Card|