Larissa players celebrate after reaching the group stage Blackburn came from behind to beat Larissa but were knocked out of the Uefa Cup 3-2 on aggregate and miss out on the group stage of the competition. Larissa scored a crucial goal when Cleyton converted from 12 yards after creating space with a neat sidestep.
Rovers equalised with a Matt Derbyshire penalty after keeper Elias Kotsolis brought down David Dunn.
Stephen Warnock then finished superbly for Rovers early in the second half but Larissa held out to win the tie.
Interview: Blackburn boss Mark Hughes
It was a valiant effort by Rovers after the break, with David Bentley particularly threatening.
But they ultimately paid for a poor performance in Greece, where they lost 2-0, and a disappointing first-half showing at Ewood Park.
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The visiting supporters made the bulk of the noise in the opening stages - and the volume increased further when their team took the lead.
Cleyton was left in far too much space after collecting Panagiotis Katsiaros' cross from the left and had time to place his shot in the bottom corner.
The Larissa striker underlined his goal threat again later in the half, eluding Dunn but drilling his strike wide of Brad Friedel's goal.
Rovers, unchanged from the team that beat Sunderland in the Premier League, started the tie poorly and were caught offside on several occasions.
But the home team did eventually threaten after 27 minutes when Chris Samba got the better of former Leicester and Newcastle defender Nikos Dabizas only to direct his header over the crossbar.
Dunn should have done better after being played in by Tugay but his first touch was heavy and he could not get the required power on his effort, while Derbyshire later pulled a shot wide.
Derbyshire equalised for Rovers from the penalty spot
And Larissa, playing with great composure and confidence, threatened again through Nektarios Alexandrou, whose shot on the half-volley was deflected wide.
But when it seemed as though Blackburn would go into the break with their European hopes all but extinguished, they pulled a goal back.
Kotsolis was perhaps harshly adjudged to have brought down Dunn and Derbyshire slotted home the spot kick at the second attempt.
The Larissa keeper saved the first effort but only after illegally advancing off his line.
And six minutes after the start Warnock's excellent finish put Rovers ahead on the night after he latched on to a ball forward by Bentley.
Rovers poured forward, with Derbyshire just failing to convert a cross from Warnock and the Greek team struggling to contain Bentley.
Blackburn brought on Morten Gamst Pedersen and Benni McCarthy and the home team created several half chances.
Samba looped a header over the keeper but also over the crossbar.
And as the match wore on Larissa gradually regained a measure of control after coach George Donis brought on an extra defender and played out the final minutes for a famous aggregate victory.
Blackburn boss Mark Hughes: "If we are honest over the two legs we left ourselves with too much to do. "Fair play to the lads, we kept going and won the game and that is a positive but we are disappointed as we have enjoyed our games in Europe.
"Good luck to Larissa, they played well over the two legs."
