James Davies produced a man-of-the-match display as the Welsh side recorded a 23-13 victory - preserving their 15-month unbeaten run at Parc y Scarlets.
Leinster held a two-point lead at half-time thanks to Ben Te'o's powerful try but scores from Jordan Williams and Rory Pitman condemned them to defeat, meaning they have now won just one of their last four league games and drop to fifth place in the league.
O'Connor made nine changes from the side that drew 9-9 with Ospreys last weekend, welcoming a number of players back from international duty, and acknowledged that his side lacked cohesion.
But the former Australian international was keen to credit the opposition for a well-executed gameplan.
"I thought the whole Scarlets side played well," said O'Connor. "I thought the Scarlets looked after the ball a bit better and we did not get the speed of release we wanted.
"We turned over the ball too many times when we were starting to create pressure which meant we did not get any reward for our good work.
"As a team they played well, took their chances and exposed us on the edge a couple of times and they were deserving of the result.
"It does make it more disappointing with that quality we had on the field, but we have not had those guys for a lot of time over the last eight weeks or so.
"It meant we were a bit disjointed and the line-out did not function as we would have liked it to. We did not have the scrum dominance we thought we may have either.
"So the quality was there but the performance wasn't and in this league you know you do not win with a sub-standard performance and that was the case here."
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