Leinster said that the Ireland global flanker was suffering from tightness in his calf and a decision was taken "not to risk the injury further".
Hooker Owens, who is set to tour New Zealand with the British & Irish Lions this summer, suffered an ankle injury in training this week and won't run out in the Irish capital.
Scotland back-row John Barclay returns from injury to captain the side in captain Owens's absence, while flanker James Davies also returns.
Leinster topped the PRO12 for most of the season and boss Leo Cullen has named a strong team for the semi-final clash, even with Ireland's global lock Devin Toner dropped to the bench. "We haven't been in this position since this group of coaches, and players, have been together".
Scarlets head coach Wayne Pivac said his side faced a "big task" against a side that beat them 45-9 at the RDS Arena in March. They're scoring a lot of tries themselves at the moment and it makes them a pretty complete package.
"But it's a challenge and an opportunity we are relishing".
Quand il était critiqué par ses ministres sur Twitter — Emmanuel Macron
Cette enquête a été réalisée en ligne les 16 et 17 mai auprès de 999 personnes de 18 ans et plus, selon la méthode des quotas. Ce dernier est le plus jeune du gouvernement à porter le titre de ministre, et aussi le premier né dans les années 80.
"We're not far off having our top side available, we're going in there with some confidence, not over-confident, but confidence that we deserve to be there and we're going to enjoy the occasion".
Ross Byrne has taken O'Brien's place on the Leinster replacements bench.
Jack McGrath, James Tracy, Tadhg Furlong, Ross Molony, Hayden Triggs, Rhys Ruddock, Josh van der Flier, Jack Conan.
Scarlets: Johnny Mcnicholl; Liam Williams, Jonathan Davies, Scott Williams, Steff Evans; Rhys Patchell, Gareth Daviess; Rob Evans, Ryan Elias, Samson Lee, Lewis Rawlins, Tadhg Beirne, Aaron Shingler, James Davies, John Barclay (capt).
Replacements: 16Emyr Phillips, 17 Wyn Jones, 18 Werner Kruger, 19 David Bulbring, 20 Will Boyde, 21 Jonathan Evans, 22 Hadleigh Parkes, 23 DTH van der Merwe.
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