Scarlets produced a gritty effort in difficult conditions before going down 12-3 to a Springbok-stacked Sharks team in Durban.
Scarlets went toe to toe with their hosts for the full 80 minutes, but an error-strewn contest was ultimately decided by the boot.
Holding a losing bonus point until the final minute it looked like the Scarlets would be heading back to South Africa to take on the Vodacom Bulls in the quarter-finals.
But a penalty by full-back Aphelele Fassi with the last kick of the match sent them to Dublin to take on top seeds Leinster instead.
On the back foot for long periods and heavily penalised, Scarlets’ produced a resilient defensive effort, but the chances they did create they were unable to capitalise on.
Scarlets went into the round 18 clash having already secured a place in the knockout stages courtesy of results on Friday evening. All that remained was finding out where they would be flying to in the last eight.
The Welsh side needed some stubborn defence to keep out the Sharks in a scoreless opening quarter, the highlight for the visitors being a rampaging run by Vaea Fifita from halfway.
The humidity in Durban made for greasy conditions at Kings Park and it led to a mistake-ridden first half from both sides.
Despite being under pressure for long periods, the Scarlets almost claimed an opportunist breakaway when Joe Roberts, making his 50th appearance, pounced on a loose ball before feeding Archie Hughes, who sped away. However, the young nine just couldn’t find half-back partner Sam Costelow with the try-scoring pass.
The deadlock was eventually broken when fly-half Siya Masuku landed a penalty from straight in front, but back came the Scarlets, turning the ball over to allow Costelow to land a smart drop goal off his left foot.
With the Sharks forwards coming more into the game, inspired by Boks star and player of the match Eben Etzebeth, full-back Aphelele Fassi put the Sharks in front on 52 minutes. The South African international then made it 9-3 with 12 minutes remaining as Sharks looked to take some sort of grip on proceedings.
Scarlets did have a late opportunity from an attacking line-out, but the Sharks were able to sack the drive and eventually clear their lines.
In the final minute, with the Sharks forwards pounding forward, referee Andrea Piardi awarded another penalty in front of the posts and Fassi made no mistake with the final kick of the match.
It means the Scarlets will take on tournament pacesetters Leinster in their quarter-final at the Aviva Stadium on Saturday, May 31, kick-off at 3pm.
Sharks – pens: S. Masuku, A. Fassi (3)
Scarlets – dg: S. Costelow