Only Lifeimi Mafi, Mick O'Driscoll and stand-in captain Denis Leamy remained from the Munster team that beat Brive in Europe last weekend.
But Tony McGahan's much-changed side still had too much for the Scarlets who leaked the only try of the game to Simon Zebo, 13 minutes from time.
The young winger pounced when a Scarlets move broke down and hacked through twice before dotting down in the left corner.
The victory ensures Munster will sit top of the Magners League at the end of the regular season, while the defeat ends the Scarlets' hopes of making the last four.
The visitors came into the match needing just a point to secure a semi-final back at Thomond Park, while the Scarlets, who lost at Ulster last time out, were desperate for a win to reignite their chances of featuring in the play-offs.
Both sides had their chances in a frenetic opening. Wales winger George North knocked on with the try-line beckoning while the lively Zebo was hauled down just short after a fine break from inside his own half.
A penalty by out-half Rhys Priestland gave the home side the lead after 19 minutes, but the Scarlets were struggling to get their fluid game going against some typically aggressive Munster defence.
And after winning a penalty at a Scarlets scrum, Munster were level through the boot of full-back Paul Warwick just before half-time.
The Australian then added a second following some good foraging from the visitors' pack, giving his side a 6-3 interval advantage.
Priestland missed with a chance to level matters four minutes into the second half, but the Scarlets continued to press hard despite the miss.
And when the Scarlets pack shoved Munster's eight back at a scrum, Priestland had another shot at the posts and this time was on target to level things up again.
The Scarlets were denied a try when Scotland winger Sean Lamont was held up on the line by a fine tackle from Leamy as Munster, driven on by the snappy Peter Stringer, continued to frustrate the home side.
In a hard-fought, defence-dominated half, McGahan's men almost claimed a try of their own, only for young winger Danny Barnes to be shoved out in the corner.
They were not to be denied though, with former Ireland Under-20 international Zebo grabbing the match-winning score.
The Scarlets looked to run the ball out of defence, Regan King was swarmed over by Munster tacklers and Zebo needed no second invitation as he created his opportunity and finished it well.
Warwick calmly threaded the conversion through the posts to make it a seven-point game and give Munster a sudden level of comfort.
Priestland was off target with a penalty attempt and despite some concerted attacks from deep, the Scarlets could not break down a durable Munster pack that was bolstered in the second half by old hands John Hayes and Alan Quinlan.
The Scarlets had some strong individual performances, most notably from full-back Morgan Stoddart, prop Iestyn Thomas and flanker Rob McCusker.
But they were left reflecting on missed scoring opportunities at the finish, and their head coach Nigel Davies summed up the mood in the camp.
"I felt in the first half we could have taken control of that game if we'd been more accurate. We had lots of opportunities and didn't take them," he said.
"It was a big game and there was a big crowd there for us. In the second half Munster came back into the game, and they have the mentality they believe they can win wherever they go, and that's what they did.
"It was a big test for this team today, to come up against of a side of Munster's quality but more than anything else it was a test of our players' mentality, their winning mentality.
"This team play with great spirit and commitment and have done all season, you can't fault them. But there's a line that this team have to cross at the moment and that's to get into the winning habit. We haven't crossed that line yet."
|Scarlets Score Card|
|Munster Rugby Score Card|