James Coughlan's second-half try while Johnathan Edwards was in the sin-bin, allied to four penalty goals from Ronan O'Gara, kept the province's European challenge on the rails at Thomond Park.
Scarlets hit back with a converted try from replacement Ken Owens and had they been able to convert more of their chances, they may have had enough momentum in the final quarter to spring a surprise result.
But Nigel Davies' young side could not make use of their greater share of possession and streetwise Munster have now tightened their grip on Pool One ahead of the two final rounds.
Stephen Jones, whose inclusion saw Rhys Priestland revert to full-back, sparked the opening attack for Scarlets but Munster were first on the scoreboard, Gareth Davies' obstruction of Coughlan under a high ball allowing O'Gara his first shot at goal.
Jon Davies and the industrious Rob McCusker led the visitors' charge back into the Munster 22, setting up a right-sided penalty which Jones drilled over in the 13th minute.
Punchy runs from Matthew Rees and Gareth Davies kept the Munster defence busy, and a bulldozing break from centre Davies off lineout ball gave another warning as to Scarlets' ball-carrying strengths.
Crucially though, Munster quickly cut down the options and they gradually got their pick-and-go game going with Paul O'Connell, BJ Botha and Coughlan barging into the Scarlets 22.
Handling errors spoilt some promising approach work from both sides in a forgettable, mistake-ridden first half, and it took a forceful scrum from the home pack to tee up O'Gara for his second penalty and a 6-3 lead.
Scarlets had an immediate chance to reply but Jones' radar was off, drawing his 37th-minute kick to the left and wide, and Munster's tight five ended the half with some muscular drives.
Simon Zebo was hauled down just metres out and having been well tackled, gave away a penalty in his desperate attempt to reach the Scarlets line.
Into the second period, Priestland was moved to out-half to cover for Jones who sustained a neck strain and the tale of two number 10s continued as O'Gara watched a penalty effort come back off the right post.
The Heineken Cup's record points-scorer redeemed himself with a successful kick from a similar range, two minutes later, although Scarlets hit back with good bursts from Ben Morgan and Jon Davies.
Priestland, however, missed a kickable penalty and in the space of three minutes the Celtic encounter swung in Munster's favour.
Man of the match Conor Murray gained great ground on a jinking run from deep, offloading superbly for Damien Varley to power forward. O'Connell and company added further momentum to the attack and Scarlets flanker Edwards sacrificed himself by infringing at a ruck with a Munster try on the cards.
O'Connell claimed the resulting five-metre lineout and the Welsh defence could not hold out as Coughlan drove over, with O'Gara adding the extras for what looked a decisive 16-3 advantage.
Priestland rallied his troops with a much-needed three points and some ferocious defending kept Munster out as they inched forward in front of the Scarlets posts. A fourth successful penalty from O'Gara was the province's only reward.
Scarlets had a near miss when Denis Hurley fumbled a bouncing ball near his line and the returning Edwards was almost in. They kept the pressure on and with Morgan providing the grunt off the back of a scrum, Owens burrowed over from a ruck for a 66th-minute try.
Priestland knocked over the conversion, whittling Munster's lead down to six points and the introductions of Owens, Phil John and Sione Timani had clearly energised Scarlets as they started to take the game to Munster.
Munster's defence held out despite some strong runs from Timani and Davies again, and a knock-on from Tavis Knoyle let the home side off the hook. Further Scarlets errors in contact, coupled with a last-minute yellow card for Rhys Thomas, saw Munster soak up the pressure and take yet another tight verdict in front of a relieved home crowd.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.