Under their previous guise, the west Wales side had never beaten the Irish province, and to record the win at fortress Thomond Park is a feat that means the Scarlets are considered serious championship contenders.
The win brings Munster's amazing eight year unbeaten run to an end, closing a chapter on one of the great sporting records.
Scarlets outside-half Gareth Bowen almost single-handedly destroyed that record, scoring all the points with a try and 14 points from the boot.
Neither side could register a five-pointer in the first period, Munster taking a three-point lead into the interval thanks to Jeremy Staunton's two penalties compared to Bowen's solitary effort.
In the second period, Bowen dropped a goal to level the scores, and after the sides exchanged penalties, a tense finale was ensured.
When the ball broke loose from a charged-down kick, it was that man Bowen who has the legs to collect the ball, and touch down for the games only try.
Munster rallied, and Staunton narrowed the gap with a penalty, but when Bowen scored a fourth penalty in extra time, the game was up, as was Munster's record.
A delighted Scarlets captain Leigh Davies was keen to praise his young team after the historic win.
'If you could see the delight on the boys faces in the dressing room - a lot of them are young and haven't seen anything like that,' Davies told BBC Wales Sport.
'They had 12 internationals out, but we were missing 10.
'We've got a great squad here and the World Cup boys will have to fight for their places when they get back. Gareth Bowen was outstanding'
Munster (6) 12, Llanelli Scarlets (3) 19 (Thomond Park)
Munster: J.Staunton; M.Lawlor, M.Mullins, J.Jones-Hughes, S.Payne; K.Keane, E.Reddan; S.Kerr, J.Flannery, M.Cahill; T.Hogan, E.Halvey; D.Leamy, D.Wallace, J.Williams (capt).
Bench: M.McPhail, C.McMahon, F.Murphy, S.Keogh, D.Sheehan, A.Long, J.Danaher.
Llanelli Scarlets: B.Davies; T.Selley, M.Watkins, L.Davies, D.Burn; G.Bowen, M.Phillips; D.Maddocks, A.Gravelle, J.Davies; A.Jones, C.Wyatt; E.Lewis, I.Boobyer, S.Quinnell.
Bench: N.Williams, R.Williams, B.Griffiths, V.Cooper, L.Byrne, C.Thomas, G.Evans.
Scorers: Bowen(1T, 1C, 3PG, 1DG).
Referee: G Davies Attendance: 5500.