Rhys Priestland opened the scoring with a penalty in the 18th minute, Warwick levelled in the 39th and then kicked Munster into the lead.
Priestland levelled again but when Scarlets spilled the ball inside their own half in the 68th minute, Zebo kicked ahead and easily won the race to the touchdown.
It was a victory that secures Munster a home semi final in the Magners League play offs.
Munster: P Warwick; S Zebo, J Murphy, L Mafi, D Barnes; D Cusack, P Stringer; M Horan, M Sherry, S Archer; D Ryan, M O'Driscoll; T O'Donnell, N Ronan, D Leamy capt. Replacements: D Fogarty, D Hurley, J Hayes, A Quinlan, P Butler, D Williams, S Tuitupou, S Deasy.
Scarlets: M Stoddart; G North, R King, G Maule, S Lamont; R Priestland, T Knoyle; I Thomas, M Rees capt, R Thomas; L Reed, J Turnbull; R McCusker, J Edwards, D Lyons. Replacements: E Phillips, R Jones, S Gardiner, A Shingler, D Welch, G Davies, S Jones, S Williams.
Referee: Alan Lewis (Ireland).