In the other top of the table clash, Ospreys defeated Gwent Dragons to inch ever so closer to the League title.
In Musgrave Park, Paul Burke opened the scoring with a penalty after just five minutes as the home side dominated territorially.
They were rocked however in the 7th minute when both David Wallace misjudged a Tommy Bowe 'garryowen' and Bowe collected to score on the left.
The Munster response was immediate and John Kelly was on the end of a slick move to score his side's opening try.
Paddy Wallace levelled with a well taken drop goal and Roger Wilson put the northeners ahead with a 35th minute try on another rare Ulster incursion into the Munster half.
In injury time Munster probed left through Mike Mullins and when they put the ball thtrough hands going right, Alan Quinlan off-loaded superbly to Wallace who stepped inside to score.
Munster once again dominated in the second half but had just two penalties from the superb Burke to show for their efforts.
Overall Burke enjoyed one of his best performances of the season. He was helped by a marvellous service from Frank Murphy who deservedly won the Toyota Man of the Match award.
Munster. Shaun Payne; John Kelly, Mike Mullins, Rob Henderson (Jason Holland), Anthony Horgan; Paul Burke, Frank Murphy; Frank Roche, Jerry Flannery, Gordon McIlwham (Eugene McGovern); Trevor Hogan, Tom Bowman; Alan Quinlan, David Wallace, Jim Williams capt (Stephen Keogh).
Ulster: Bryn Cunningham; Tommy Bowe, Seamus Mallon, Paul Steinmetz, Tyrone Howe; Adam Larkin, Kieran Campbell; Ronan McCormack, Paul Shields, Rod Moore; Gary Longwell, Matt McCullough; Andy Ward, Neil Best, Roger Wilson.
Replacements: Nigel Brady, Bryan Young, Tim Barker, Campbell Feather, Neil Doak, Scott Young, Shane Stewart.
Referee - Andy Ireland (SRU).