A misfunctioning line-out cost the Scarlets a fine win at Musgrave Park.
Munster (8) 14
Pens: O'Gara (3)
Scarlets (13) 13
Tries: Byrne, Watkins
Debutant wing Ian Dowling got the home side off to a perfect start with a try as returning Lion Paul O'Connell ruled the roost at the set piece.
But the Scarlets' backs fired back with tries from Lee Byrne and Matt Watkins to give them a 13-8 half-time lead.
Pressure mounted as the visitors lacked possession and Ronan O'Gara's boot put Munster ahead, before Mike Hercus' late penalty miss sealed the Scarlets' fate.
O'Gara gave Munster the lead with a penalty and, after the pack stole Scarlet line-out ball, the fly-half's delicate grubber kick led to the first try.
Alan Quinlan competed with Dafydd James for the touchdown, but both missed it to allow Dowling to claim his first score for Munster.
But the Scarlets' backs had looked threatening whenever given the ball, and when James made inroads into the midfield Hercus and Regan King combined to send Byrne over for the Welsh side's first try.
Frankie Sheahan looked to have been denied a good try after a rolling maul from a five-metre line-out, and Munster were punished further soon after.
Excellent driving work from Aled Gravelle delivered front-foot ball to Hercus, who again combined with King to send Watkins over.
Hercus missed both conversions, but landed a long-range penalty on the stroke of half-time to stretch the visitors' lead to five points.
That looked to have been extended early in the second period when King combined brilliantly with Hercus to send the fly-half under the posts, but the Kiwi's final pass was controversially ruled forward.
Clive Stuart-Smith gets the ball away under pressure
Line-out problems continued to plague the visitors and under the pressure two O'Gara penalties saw Munster retake the lead, the second also leading to a yellow card for Adam Jones.
Heroic defence from the 14-man visitors then held out the rampant Irish, and with three minutes to go Munster's John Hayes was sin-binned for foul play.
More indiscipline from the Irish at a line-out gave Hercus a golden chance to snatch the win with a 35m penalty, but the USA international sent his kick wide.
Scarlets director of rugby Gareth Jenkins:
"We were by far the better team in the first half, but didn't do enough after the break to justify the opportunities we created.
"Our line-out felt the pressure and didn't deliver the ball, then the disallowed try broke us.
"I've always said that this is a new and growing team. I'm pleased with the way we are developing and feel that there is a lot more to come."
Munster: B. Murphy, Kelly, Leamy, Halstead, Dowling, O'Gara, O'Leary, Pucciariello, Sheahan, Hayes, O'Callaghan, O'Connell, Quinlan, Wallace, Foley.
Replacements: Henderson for Leamy (41), Horan for Pucciariello (77), O'Driscoll for O'Connell (75). Not Used: Flannery, Hogan, Prendergast, Burke.
Scarlets: Byrne, James, Watkins, King, Selley, Hercus, Stuart-Smith, I. Thomas, Gravelle, J. Davies, Louw, A. Jones, Easterby, Mills, A. Popham.
Replacements: L. Davies for Stuart-Smith (74), Wyatt for Louw (47). Not Used: Williams, Hawkins, Quinnell, Bowen, Daniels.
Referee: Andy Ireland (SRU)