Both sides committed multiple errors in attack as both defences excelled, Saracens struggling to execute at the lineout in one of the most physical encounters witnessed so far this season.
Owen Farrell missed four shots at goal on a bad night for the England fly-half to deprive Saracens of a famous victory, with Munster's win leaving Pool 1 of the Heineken Cup wide open after Racing Métro's victory over Edinburgh.
The physicality of James Coughlan alongside Peter O'Mahony proved to be the difference but Saracens came away from Thomond Park with an important losing bonus point ahead of next weekend's return fixture.
Munster started in ferocious fashion, scrum-half Conor Murray bursting through the Saracens defence but his pass to David Kilcoyne went forward under pressure in front of the posts.
Ronan O'Gara then added the first points of the afternoon in the fourth minute to give Munster an early lead, before Owen Farrell failed to convert his first opportunity of the match, a poor strike seeing the ball come off the pad of the post.
Munster conceded six penalties within the opening 20 minutes as they persistently infringed at the breakdown whilst on the attack to deprive them of valuable scoring opportunities.
A brawl moments later saw both Rhys Gill and Donnacha O'Callaghan sent to the sin-bin as the tension between the two sides boiled over.
A penalty this time against Saracens at the breakdown presented O'Gara with a second opportunity to kick at goal, which he duly took to stretch the lead to 6-0 coming up to 30 minutes gone, both sides returning to 15 men as Gill and O'Callaghan returned.
The visitors struggled to maintain their accuracy at the lineout when in Munster territory, but Saracens won a penalty from a scrum deep in Munster's half for Farrell to kick their first points of the match.
O'Gara responded after Munster won a penalty at the lineout, leaving the scoreline at 9-3 just before half-time.
Saracens were handed an early opportunity to put points on the board at the start of the second half with another Farrell penalty, but the England's fly-half's attempt fell short.
Farrell however was given an immediate opportunity to bounce back and did so from a much easier angle to close the gap to 9-6.
The heavens opened as Munster stole a scrum against the head in the Saracens half and won a penalty kick for O'Gara to increase the lead once more.
Confusion in the Saracens defence after a Munster box kick led to the ball being hacked on by O'Callaghan with Munster winning a scrum on the edge of the Saracens 22, winning another penalty from the resulting attack as Steve Borthwick was warned by referee Pascal Gauzere. O'Gara made no mistake with his shot at goal.
A loose pass however from Conor Murray sent Munster back pedalling with Doug Howlett penalised at the resulting ruck, but Farrell was unable to convert the resulting penalty.
Both defences continued to hold firm forcing the opposition into marginal errors in attack, but a driving maul from Saracens within the Munster 22 resulted in an overlap down the right hand side, only for openside flanker Will Fraser to be bundled into touch inches from the line.
Owen Farrell moving infield to fly-half gave Saracens fresh impetus in attack but Munster continued to force them into errors, with Farrell then missing another penalty kick at goal to leave him with only two attempts from six and keeping Saracens out of losing bonus point range.
A lineout outside the Munster 22 handed Saracens one final chance to get more points on the board and from a penalty at the lineout Farrell was successful with his seventh attempt of the afternoon, leaving the score at 15-9.
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