Tries from CJ Stander, Andrew Conway and Dave O'Callaghan, plus a near-impeccable kicking performance from Ian Keatley secured the points for the home side.
And despite a brief flurry from the visitors in the final few minutes - in which skipper Shane Jennings dived over the line - Munster never looked like losing the contest and secured their first league double over Leinster in six years, moving to the top of the GUINNESS PRO12 in the process.
But O'Connor insisted that a poor start and lack of intensity in the middle of the game - where the Leinstermen slipped from two points adrift to 28-6 down - cost his side on the day.
"I thought we prepared very well even given the circumstances of the week," said O'Connor. "I thought we were in a pretty good head space coming into the game.
"But we let ourselves down in that first 20 minutes and away from home, especially at a place like this, you can't afford to get it wrong the way we did in the first 20 minutes.
"That was the most disappointing thing and we didn't strangle the game back and Munster just got better and better.
"The inaccuracies and the errors took the impetus away from us and grew Munster's belief, which was probably the difference in the end.
"We just didn't exert any pressure in the middle of the game. We didn't have any field position. We didn't build any phases and they did incredibly well with the ball they had.
"Our effort was fantastic. We had to make a lot of tackles and in the second half, down a man, I thought we coped pretty well in that period.
"But it was always going to be hard at 28-6 to come back into it."
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