After suffering a 4-2 defeat in Birmingham last week, Villa made a nightmare start in Greece as Ayoub El Kaabi followed up his first-leg hat-trick with the opening goal for Olympiacos inside the first 10 minutes.
Not even four-time Europa League winner Unai Emery could orchestrate a miraculous comeback at the Georgios Karaiskakis Stadium, and his jaded Villa outfit found it difficult to break down a resilient red and white defensive wall set up by the hosts.
El Kaabi eventually sealed a 2-0 second-leg victory for Olympiacos 12 minutes from time, scoring his fifth goal of the two-legged tie and moving onto 10 goals at the top of the Conference League scoring charts with a clinical strike beyond Emiliano Martinez.
Jose Luis Mendilibar - who led Sevilla to Europa League glory last season - only took charge of Olympiacos in mid-February, but he has successfully steered the club to their first-ever European final, with the Red-Whites becoming just the second Greek team after Panathinaikos in 1970-71 to reach a major UEFA competition final.
Olympiacos can now look forward to the Conference League showpiece in their own country at the home of their rivals AEK Athens - the Agia Sophia Stadium - where they will face Italian outfit Fiorentina on May 29.
As for Aston Villa, their hopes of reaching a first European final since 1982 are over and they will now endeavour to secure a top-four finish in the Premier League and qualify for next season's Champions League.
Nightmare start for Villa as El Kaabi strikes first
Trailing by two goals from the first leg, Villa knew they had to stamp their authority on the game early doors, and although they had a few encouraging moments in possession, it was a familiar face who struck first for Olympiacos in the 10th minute.
After Villa had pushed a few bodies forward, Wolverhampton Wanderers loanee Daniel Podence played a smart pass down the left channel for left-back Quini, who fizzed a first-time cross towards the back post for an unmarked El Kaabi to squeeze his shot beyond Martinez.
Emery's men dominated proceedings with 82% possession in the opening half-hour, but they struggled to break down Olympiacos' low block and test goalkeeper Konstantinos Tzolakis.
There was a degree of concern for Leon Bailey, a bright spark for the visitors in the first half, after he was wiped out on the edge of the area after clashing knees with Rodinei, who was booked for his offense. Bailey gingerly got back to his feet before Douglas Luiz - on his 26th birthday - floated the resulting free kick over.
Olympiacos rarely threatened at the other end until captain Kostas Fortounis tried his luck from range with a side-footed shot that was comfortably saved and gathered to the left of Martinez.
Bailey was at the heart of almost every Villa attack and he rolled an inviting delivery across the six-yard box that was begging to be tapped in, but Matty Cash failed to anticipate the cross and was late to arrive at the far post. The Jamaican was then denied from around 30 yards by the strong hands of Tzolakis.
El Kaabi sparks party in Piraeus as Olympiacos make history
It took just four minutes after the break for Villa to put together their first free-flowing move in the final third, but it ended in disappointing fashion as Ollie Watkins could only float is header onto the roof of the net.
Villa's tempo briefly dropped and frustrations grew as they produced a few wayward passes, but they gradually grew back into the contest and enjoyed an extended spell of possession inside Olympiacos' half.
The better chances arguably fell to the hosts, though, with El Kaabi firstly overhitting an unselfish pass towards the run of Santiago Hezze and the back post, before being denied a header from close range by the outstretched leg of Ezri Konza, who was alert to get in front of his opponent and clear the danger.
Villa continued to push forward in search of a goal, but Olympiacos landed the knockout blow on the 78-minute mark when El Kaabi burst through on goal and smashed a left-footed shot beyond Martinez - the Moroccan's celebrations were briefly delayed, but VAR confirmed the goal following a review for offside.
It is hard to believe that El Kaabi is enjoying his first-ever European campaign, but at the age of 30, the summer signing from Al Sadd has now netted 15 goals in 18 appearances for Olympiacos across the Europa League and Conference League (including qualifiers), while he has scored 32 goals in 46 games across all competitions.
Olympiacos eventually cruised to a deserved aggregate victory and will now shift their focus back to domestic duties, with a trip to PAOK in the Greek Super League up next on Sunday, a day before Aston Villa play host to Liverpool in the Premier League.