Doug Howlett scampered over for a try and the home pack also earned a penalty try as Munster took a 20-9 lead into the break.
Four penalties from Dan Newton and a monster effort from debutant Dale Ford kept the Scarlets in contention.
But the Munster bench had a considerable say in the closing stages, with replacements Duncan Williams and Tommy O'Donnell helping themselves to tries.
Johne Murphy had to show quick reactions to get back and dot down for a dropout after Rhodri Gomer-Davies had launched a kick chase in the opening seconds.
The Scarlets forced the early pace, an offside decision allowing Newton to kick them ahead and a slashing run from Lee Williams also signalled their attacking intent.
Ian Keatley launched over his first penalty of the night, drawing the sides level in the 10th minute, before Howlett raced away for his try.
Munster pounced on a loose ball near halfway and a neat thread of passes between Mick O'Driscoll, Peter Stringer and Peter O'Mahony allowed the former All Black to evade Dominic Day's despairing tackle and score in the right corner.
Keatley swung over the conversion and traded further penalties with Newton, with the game cantering along at a brisk pace and both sides eager to move the ball wide.
On the half-hour mark, Munster showed their experience in a set of five-metre scrums, and when Rob McCusker interfered illegally with the ball still in a scrum, referee Andy Macpherson signalled for a penalty try.
Keatley added the extras from in front of the posts, but teenage Scarlets full-back Ford answered back with a tremendous 55-metre penalty.
The pace dropped in a rain-hit second half. Newton landed his fourth successful penalty and television match official Jude Quinn adjudged Marcus Horan to have been held up short on a close-range drive.
The worsening conditions contributed to a number of handling errors, Mike Sherry and Ruki Tipuna both dropping balls they would normally take. Ford then missed a chance from long distance to make it 20-15.
The Welsh region were still very much in the hunt but an advancing Munster scrum, strengthened by the introductions of South African duo Wian du Preez and BJ Botha, won a penalty which Keatley duly knocked over.
A killer blow for the Scarlets came when Munster worked a lineout maul and Sherry's simple pass off the side sent scrum-half Williams haring over for an unconverted try.
With Munster's 12th successive win over the Scarlets confirmed, O'Donnell added the icing on the cake by storming over in the right corner. Keatley converted and the title holders returned to the top of the table.
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