Both sides suffered withdrawals before kick-off. Llanelli's influential number eight Scott Quinnell missing out because of a groin injury while Munster skipper Jim Williams had to return home because of a family illness.
Adrift by 17 points at the interval, many of the home fans in the 6,169 crowd felt the Munstermen were dead and buried, but with scrumhalf Eion Redden at the hub of a major, wind assisted revival after the break the visitors clawed their way back to within seven points fifteen minutes from time.
Munster struggled in the first half when they played into the strong wind. The also struggled to contain the direct running of centre Mathew Watkins.
The Wales international notched the first of the game s seven tries after half an hour while Munster were reduced to fourteen men with number 8 Stephen Keogh in the sin-bin.
The home side scored 10 points with Keogh off the field and were 20-3 to the good at half-time thanks to a second try from former Wales wing Richard Rees.
But it was a different story in the second period.
Munster, with a bitterly cold wind at their backs, first hit back with a fine solo score from scrum-half Eoin Reddan before Horgan's double strike set up a grandstand finish.
But it was Scarlets and Bowen who finished the stronger with the fly-half sealing the five points - and a rare double over Munster - with his late flurry.
Final Score: Llanelli Scarlets 37 Munster 20
Scarlets (37) Tries: G Williams, Rees, Watkins, G Bowen Cons: G Bowen 4 Pens: G Bowen 3
Munster (20) Tries: Horgan 2, Reddan Cons: Henderson Pens: Henderson
Munster: S Payne; J Kelly, J Jones-Hughes, R Henderson, A Horgan; J Holland, E Reddan; S Kerr, J Blaney, G McIlwham, T Hogan, D Pusey, P Malone, E Halvey, S Keogh.
Replacements: M Lawlor, C O'Sullivan, F Murphy, F Roche, J Flanery, D Sheahan, T Hayes.
Scarlets: B Davies; R Rees, T Selley, M Watkins, R Johnson; G Bowen, M Phillips; P John, A Gravelle, J Davies, V Cooper (capt), C Wyatt, E Lewis, G Williams, D Hodges.
Replacements: M O'Kelly, A Yelland, A Jones, J Griffiths, D Burn, C Thomas, D Rogers.
Referee: Graeme Hannah (Scotland)