Former Manchester City trainee Denis Suarez gave Barca a commanding lead in the tie following last week's 1-0 win in the first leg by scoring the opener in the 17th minute, while Messi practically ended the contest by converting a penalty early in the second half after Neymar had been fouled.
Luis Suarez restored Barcelona's two-goal lead on the night a minute after Juanmi had netted for Real Sociedad in the 62nd minute. Willian Jose scored a second for the visitors before substitute Arda Turan put Barcelona 4-2 ahead in the 80th minute.
Two minutes later Denis Suarez capped a brilliant individual performance by netting his second with a sweeping run and finish.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Barca join Atletico Madrid, Celta Vigo and Alaves in Friday's semi-final draw.
Barca were without key midfielders Sergio Busquets and Andres Iniesta through injury so Javier Mascherano reassumed the holding midfield role he plays for Argentina and Denis Suarez filled in for the absent captain.
The Galician-born midfielder had scored the opener in Sunday's 4-0 league win at Eibar and broke the deadlock again with an arrowed finish into the far bottom corner following clever interplay between Messi and Luis Suarez.
Barca looked in control for the remainder of the half, but were inches away from conceding an equaliser shortly after the break when Willian Jose burst into the box but fired straight at reserve goalkeeper Jasper Cillessen.
Barca went on the attack immediately and Neymar terrorised the visiting defence, winning a deserved penalty as he was tripped by Inigo Martinez.
The Brazilian had won and scored the decisive penalty in the first leg but surrendered spot kick-taking duties to Messi, who sent the ball beyond the reach of compatriot Geronimo Rulli.
Real Sociedad needed three goals at this point to cause an unlikely upset. They managed two, but every time they went forward they left themselves exposed, and Barca took full advantage.
"We started the game by dominating and once it was 1-0 they left us plenty of space and everything is easier when you have the three forwards we have," Denis Suarez told reporters after a fifth consecutive win in all competitions for the Catalans.
"We weren't nervous at all, we just wanted to dominate the game and continue on this great run that we're on."
(Reporting by Richard Martin, editing by Pritha Sarkar/Toby Davis)
