A gigantic Paul Warwick kick 10 minutes into injury time ensured the Scarlets' turbulent week continued.
The replacement Munster fly-half kicked a last-gasp penalty from inside his own half to win at Stradey in the Scarlets' first game since Phil Davies' sacking.
Tries from Dafydd James and Matthew Watkins gave the Scarlets a 20-5 half-time lead but Munster showed why they are Heineken Cup finalists.
Warwick and Ian Dowling twice inspired the Munster fight-back with tries.
Wales fly-half Stephen Jones had led by example for his beloved Llanelli, kicking 13 points as the Scarlets skipper attempted to help his men end a difficult week on a high.
The players responded well after a difficult week
Scarlets assistant coach Robert Jones
But the Scarlets could not cope with Munster's late onslaught, despite some heroic Scarlets defence, as the impact of the previous seven days took its toll on the Welshmen.
Scarlets coach Robert Jones said: "It was a game we desevred to win and that is five or six games now this season we've lost in the dying minutes.
"We wanted to show that after a difficult week we can still perform and prove to be one of the best teams in Europe.
"The players responded well as all they want to do is play rugby and we showed good continuity and skill level."
But it was Munster that raced into a fourth-minute lead as Ian Dowling touched down for the fourth time this season.
But the Scarlets responded just how caretaker coach Paul Moriarty would have wanted and it was his captain who led the charge.
The experienced Stephen Jones nudged the Scarlets in front as the Wales star landed two successful penalty kicks.
The hosts then took advantage of the wind at their backs and a one-man advantage with a quick-fire try double.
Lions and Ireland flanker David Wallace had been sin-binned in the 21st minute for lying on the ball and the Scarlets capitalised.
Veteran winger Dafydd James scored his third try in as many games against Munster in the 28th minute.
Then Watkins stretched the Scarlets' lead three minutes later with a stunning solo run to score his first try in almost seven months.
Watkins proved himself the hero at both ends of the field as a last-ditch tackle on marauding forward Wallace saved a certain score before the interval.
Wallace had beaten James for pace and was all set to score before Watkins put his body on the line to save the Scarlets.
Ronan O'Gara had been guilty of missing two kicks, a conversion and a penalty, before the Ireland international eventually found his range with a relatively straight-forward penalty early in the second-half.
Munster rallied after the break and a second score from Dowling, scampering over the line after Stephen Jones had missed touch with a kick, dragged Munster back into contention.
The winger was set free by replacement prop Federico Pucciariello and Dowling made no mistake in the corner.
O'Gara, though, continued his disappointing day with the boot as his conversion hit the post.
Jones showed his old Lions fly-half rival how it should be done as Wales' Grand Slam hero successfully kicked into the wind and between the posts just before the hour.
The Scarlets defence showed its muscle as Munster relentlessly pounded the Llanelli line in the dying minutes with some immense tackling.
But the sea of red eventually parted after a thorough bombardment as Warwick was sent over in the corner.
Deep into injury time, the Scarlets thought they had escaped with victory when Warwick fired his tricky touchline conversion against the upright.
But rookie Scarlets forward Lou Reed paid the ultimate price for his naive indiscipline as he was sin-binned in the 10th minute of injury time for holding onto the ball.
But crucially Reed's error allowed Warwick a kick at goal. From 50 yards and in dramatic style, Warwick did not disappoint.
Llanelli Scarlets: Stoddart, James, G. Evans, Brew (Daniel, 58), Watkins, S. Jones (Priestland, 80), Cattle (Davies, 58), I. Thomas (John, 66), Rees (Schwalger, 64), Manu, Cooper, MacLeod (Reed, 70), D. Jones, G. Thomas, N. Thomas (Bater, 56).
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