Anthony Foley's men built an 11-6 interval lead in Limerick with CJ Stander crossing for a 16th-minute try.
Andrew Conway came back to haunt his former team with a well-taken try in the 44th minute and during Darragh Fanning's sin-bin period, Munster replacement Dave O'Callaghan collected try number three before Ian Keatley capped off his 13-point kicking haul.
Stand-in captain Shane Jennings responded with Leinster's lone try, but they could not avoid their first league defeat since Munster visited them in early October.
Biggar boosts Ospreys to victory
The Irish Rugby Football Union player welfare programme may have robbed this festive fixture of some of its headline acts - including the likes of Peter O'Mahony, Paul O'Connell, Rob Kearney and Jamie Heaslip - but it was, nonetheless, a full-blooded encounter.
Keatley and Ian Madigan swapped early penalties, Munster forcing a maul infringement initially and then their loosehead John Ryan was pinged for not rolling away quickly enough.
Faced with bunched midfields, both kickers cleverly exploited the space in behind before the Munster pack got on the front foot with some muscular carries.
Leinster had to replace a groggy Dominic Ryan and as they adjusted, the hosts struck for the game's opening try. Stander, who temporarily lost his jersey, raced onto a Duncan Williams pass to make the line despite the presence of Luke Fitzgerald and Dave Kearney.
Keatley missed the conversion but soon threatened on an arcing run over halfway, Leinster scrambling back and then responding with a strong scrum on the hosts' 22.
Keatley was caught offside, allowing Madigan to close the gap to two points, albeit only briefly as Ryan's replacement Jordi Murphy coughed up a penalty which Keatley forced through the posts.
Madigan curled his next penalty effort wide and Leinster fell further behind in the opening minutes of the second period, Keatley's flat pass seeing Conway crash through three tacklers and he had Isaac Boss hanging off him when he touched down.
The left-sided conversion was added by Keatley to open up an 18-6 advantage and despite plenty of endeavour from Fitzgerald and Zane Kirchner, Leinster were getting little change from a resolute Munster defence.
Winger Fanning earned his yellow card for pinching a ruck ball that referee Nigel Owens deemed was not out, and that allowed Munster to dictate play approaching the hour mark.
Keatley landed the first of two penalty attempts and Foley's charges then hurt Leinster up front again, picking and carrying at close quarters until O'Callaghan evaded the grasp of both Jennings and Kane Douglas to score with 62 minutes gone.
After Keatley's conversion, Leinster managed to hit back within seven minutes. A prolonged spell of pressure ended with Jack Conan holding off JJ Hanrahan and getting his offload away for Jennings to dot down to the left of the posts.
Madigan added the extras and although both packs had sniffs of the try-line late on, impressive Munster had done enough to warrant the 15-point winning margin.
Leaders Ospreys brush aside Connacht
Sinckler cited after bad-tempered Lions defeat to South Africa