The SPL side see their European adventure end in disappointment at the hands of the Red Lightnings, who will now face French side Marseille in the next round
The first half was a largely cagey affair and dominated by the two midfields, but it was the home side who took the lead, as striker Gregory Tade headed home to reduce the deficit to 2-1 on aggregate.
The Turks came out with a great deal of attacking intent in the second half, and equalised through Veysel Sari after just six minutes, and from then on looked comfortable with their two-goal lead of aggregate and an away goal.
Saints made two changes from their 2-0 defeat away to the Turks, with Frazer Wright and Jamie Adams making way for Gregory Tade and Nigel Hasselbaink, with the inclusion of two strikers giving the home side’s formation an attacking feel.
Meanwhile, the away side made two changes of their own, as Rodrigo Tello and Burhan Eser were brought into midfield for Patryk Malecki and Batuhan Karadeniz.
The first half began cagily, with Veysel Sari picking up an early yellow card for the away side after fouling Patrick Cregg.
Sari then had the first real chance of the game in the 15th minute, but put his header straight at Saints goalkeeper Alan Mannus from six yards out, under pressure from a defender.
However, both sides were struggling to maintain possession for any length of time, and as such struggled to create many clear chances as the first half went on.
Saints created their first chance in the 25th minute, after a long punt forward from the back set striker Gregory Tade clear. However, he sent his shot wide under some pressure from an Eskisehirspor defender, and his protests for a penalty went ignored.
Them, just ten minutes later, St. Johnstone breathed some life into the tie. A cross came in from the left-hand side, and was headed in by Tade to give Saints a lifeline, and reduce their deficit to 2-1 on aggregate.
The home side almost doubled their lead just a minute later after the Red Lightnings goalkeeper Ruud Boffin spilled the ball from a free kick, almost into the path of a Saints player.
However, the danger was averted, and the first half ended with St. Johnstone up 1-0, but down 2-1 on aggregate.
St. Johnstone began the second half confidently, and nearly scored another through Nigel Hasselbaink, but his shot was straight at Boffin in the Eskisehirspor goal, and was cleared.
However, in the 51st minute, the Turks had a decisive chance, and took it. Former West Brom striker Diomansay Kamara sent a cross in from the left, and Sari was on hand to sweep the ball home, giving Eskisehirspor a 3-1 lead on aggregate, and a crucial away goal.
Saints now faced an uphill task, needing to score three goals to ensure their qualification to the next round, and just six minutes later, midfielder Liam Craig forced a smothering stop from Boffin as he was clean through on goal.
However, despite some half-chances for both sides, neither could fashion any clear openings, and Saints could not make any headway into their deficit in the face of a solid Turkish midfield.
With the full time whistle, Eskisehirspor guaranteed their progress to the next round, where they will face Marseille.