Paul Warwick added the conversion with the last kick of the game, leaving the current Magners League leaders to celebrate their first win at Ravenhill since March 2007.
Scrum half Ruan Pienaar kicked two penalties for Ulster, but blotted his copybook by missing a seemingly straightforward 77th minute kick which would have tied up the game at 9-9.
Indeed, for all their possession and territory, Ulster failed to score from the 16th minute onwards. Munster's watertight defence won it for them in the end, and their forwards punched crucial holes when opportunities arose - as shown by the maul in the lead-up to Warwick's third successful penalty, 11 minutes from the finish.
It was fourth versus first at the Belfast venue, Ulster seeking to bounce back from a disappointing outing in Edinburgh and Munster looking to make it a winning night for one of their stalwarts, scrum half Peter Stringer.
Leading the team out, Stringer became only the third player to make 200th competitive appearances for Munster, with only Anthony Foley and Alan Quinlan beating him to the milestone.
An understrength Munster side travelled north, with injuries and international commitments leaving coach Tony McGahan with a depleted squad.
Ulster were also without some of their frontliners, most notably the Ireland-tied Rory Best, Paddy Wallace and Stephen Ferris. The injured Darren Cave and Simon Danielli also missed out.
Munster, playing into the wind, knocked on from the kick-off and Ulster enjoyed a territorial advantage during a cagey opening quarter, the highlight of which was a surging run through the middle by centre Nevin Spence.
It was a rare defensive lapse by Munster. Ian Whitten took a straight line and his deft offload sent the onrushing Spence weaving towards the visitors' 22. Ulster kept the move going and winger David McIlwaine was stopped close to the left corner.
After a quick recycle, out-half Humphreys threaded a kick over to the right where Mark McCrea lurked. The ball beat him and bounced out of play, but Ulster were playing with a penalty advantage and Pienaar landed the resulting kick for a seventh minute lead.
The hosts' good work was immediately undone. They coughed up possession at the restart, with Robbie Diack and stand-in captain Johann Muller getting in each other's way. Munster's forwards built through the phases, winning a penalty close to the 22 which Warwick dispatched for 3-3.
Space was at a premium and an ill-advised kick from flanker Quinlan inside his 22 resulted a swift turnover for Ulster, with openside Willie Faloon wrestling his way forward. Humphreys ferried a long pass out to the right for Adam D'Arcy, who was grounded short of the try-line by Denis Hurley's 'man and ball' tackle.
Ulster kept pressing in and around the Munster 22 and after Quinlan was penalised for not rolling away after the tackle, Pienaar restored his side's lead in the 16th minute.
Some scrappy passages of play ensued, with neither side being able to find their rhythm. There were glimpses of quality, an angled run from Niall Ronan drawing the visiting fans' approval.
Stringer was as busy as ever, willing his forwards on. He orchestrated a counter attack on the left with an instinctive kick, but play was called back for a knock on.
There were some nice touches from Australian D'Arcy, who did all that was asked of him in difficult handling conditions.
Some good approach work by the Ulster forwards, including Paddy McAllister and Tim Barker, handed Pienaar his third shot at the posts, but this time his radar was off.
Munster sharpened up their defence in the closing stages of the half. Johne Murphy intercepted a short pass from Pedrie Wannenburg as Ulster's pack rumbled into the 22, although they were lacking the necessary penetration.
Following a wraparound move involving Humphreys and replacement Luke Marshall, Munster's stand-in skipper Doug Howlett spoilt the latter's pass with D'Arcy looming on the left wing.
6-3 ahead at the break, Ulster immediately handed the initiative to Munster by fumbling the restart kick. They then leaked an early penalty, allowing Warwick to kick Munster level from 22 metres out.
Damien Varley, who was released from Ireland's training camp for the game, began to feature more in the loose, as the Munster pack used their maul to gain ground. Ian Nagle, Ronan and James Coughlan also carried well.
Both sides struggled to find an opening as they continued to slug it out up front, Ulster bringing on debutant prop Jerry Cronin, who hails from Cork and whose father Billy ironically made his Munster debut at this venue back in 1975.
Brian McLaughlin also introduced Chris Henry and he made some headway along with Wannenburg. Ulster went through a flood of phases, trying to bludgeon their way forward.
But Munster were able to stop the central drives and use a drift defence to close down the space when the hosts passed out to the wings.
A well-timed tackle by Howlett on Spence halted a promising attack for Ulster who seemed to lack ideas, faced by this red-shirted defensive wall. In a rain-soaked final quarter, the momentum swung back to Munster.
They made the hard yards courtesy of a well-executed driving maul, forcing an infringement from Wannenburg. Up stepped Warwick to land a cracking kick from close to the left touchline, nudging the visitors into the lead for the first time.
It was a confidence-boosting score and a superb touchfinder, out to the right, from Warwick energised his forwards for one final push. Ulster were far from beaten and forced Munster into the concession of a kickable penalty.
The Ravenhill faithful anticipated the levelling kick from Pienaar's right boot, but the South African clipped his attempt narrowly to the left and wide and Munster remained in front.
Any doubts about the result were erased in the dying seconds when Pienaar's long pass from a turnover was juggled by Humphreys, under pressure from Dineen. There was no stopping the Munster number 12 after he gathered the ball from under Humphreys' nose and set off for the posts.
With the try taking a losing bonus point away from Ulster, Warwick added the simple conversion for a ten-point winning margin.
Speaking afterwards, Munster coach Tony McGahan said: "I wouldn't take anything away from them for what they got here this evening. We were missing 21 players, we were here at Ravenhill against a good Ulster side and not many sides come away from here with a result, not to mention denying them a bonus point.
"It was one of those games where we had to turn up and get the job done and we achieved that."
He added: "I thought Ivan defended extremely well, he chased hard, carried strongly and got a just reward to give us a well deserved victory.
"But overall, we asked for a huge effort from the forwards and I believe we got it. Right across the park the forwards were very good, from the set pieces to their work at the contact areas, both in attack and defence. I felt Ian (Nagle) and Billy (Holland) were among those instrumental in us getting this result."
For the third week running, Ulster boss Brian McLaughlin was left reflecting on a frustrating result. "We did a good job in the first half but didn't get points on the board when we needed them," he said.
"In the second half we were trying to chase the game, we make an error and throw away the bonus point - it's exceptionally disappointing.
"Against Munster you have to take your chances. They took theirs when it opened up for them."
|Ulster Rugby Score Card|
|Munster Rugby Score Card|