Linfield showed great character against their professional Greek opponents but they were ultimately undone by two Marcelinho strikes for ten man Xanthi, the second of these coming late in the first period of extra time.
Linfield started with summer signing Jonathan Tuffy, Sean Ward and James Knowles in their lineup.
Despite Linfield boss David Jeffery in his pre-match comments claiming it was going to be a difficult task, it was his side that started the brighter, bossing the opening quarter of an hour. On seven minutes a long Aaron Burns throw skidded across the Xanthi area and was turned around for the first corner of the game.
The first chance of the game came from this corner when the Xanthi keeper Kyriakidis flopped at the ball and James Knowles hung up a cross to the far post finding Philip Lowry but his header was tame and easily dealt with by Kyriakidis.
Linfield continued to press with Peter Thompson having an opportunity to shot on ten minutes from the edge of the area but his effort was high and wide.
Thompson was again at the centre of things five minutes later when Xanthi captain Vallas received the first yellow card off the game after he tugged the Linfield striker shirt as he strides towards the Xanthi box.
From the resulting James Knowles free kick the ball skidded of the slippery surface and just away from Aaron Burns on 20 minutes Xanthi and in particular their goalkeeper where under more pressure as another Knowles free kick was only half dealt with.
At this stage it was all Linfield who where pressing their Greek opponents high up the field and winning the 50 - 50 exchanges.
But on 23 minutes the Greeks showed their quality on the break when for the first time in the evening the pacey Mavin tested the reflexes of Jonathan Tuffy in the Linfield goals with a strike from 20 yards.
To his credit Tuffy dealt with it well. However he could do very little three minutes later when totally against the run of play the Greeks took the lead on 26 minutes Winger Marcelinho was slipped down the left he took on Jim Ervin on the outside and forced the ball between Tuffy legs at his near post for that all important away goal.
To their credit Linfield responded well with Michael Carville, Billy Joe Burns and then Peter Thompson having chances.
Indeed Thompson chance on 39 minutes was Linfield best of the half, after good play down the left by Clarke his cross was met by the head of Thompson, his flicked headed went just wide of the Xanthi far post.
Just a minute later Linfield through Jim Ervin almost pressed the self destruct button when his attempted back past to keeper Tuffy was short but the keeper did well to turn the ball away from the on-rushing Marcelinho and out for a Xanthi Corner.
On the cusp of half time Xanthi were suddenly reduced to ten men when Fliskas two-footed challenge sent Linfield striker Michael Carville tumbling, immediately the Russian referee reached for his top pocket and issued the Greek midfielder with a red card, as Xanthi took that goal lead into the break.
Linfield boss David Jeffery changed it up at half time bringing in Jamie Mulgrew for James Knowles. It was his team that started the brighter against the ten men of Xanthi with the first chance falling to Philip Lowry, his header just looping over the top from a Billy Joe Burns cross on 51 minutes.
Xanthi where on the backfoot and restricted to long range strikes as Jonathan Tuffy, similar to his role for much of the first half, was largely a spectator.
On 74 minutes Michael Gault received a yellow card for a clumsy challenge on the edge of the area and from the resulting free kick Xanthi went close through the wonderfully named Arisstide Serge Die. The Xanthi number 77 drive had Tuffy scrambling but it went into the side netting much to the relief of the large Linfield crowd.
Ten minutes later Linfield had a glorious chance to win the game as Xanthi tired.
Xanthi captain, centre-half Vallas, dwelled just too long on the ball and was disposed by Linfield sub Mark McAllister. He ran in on goal but his shot lacked the required power, despite slipping under the advancing keeper, was cleared before it reached the net by the recovering Vallas.
In the 90th minute out of nowhere having been largely outplayed in the second half Xanthi almost stole it when Vasilakakis missed a five-yard header with the Linfield goal at his mercy. Despite the late drama this tie was to be settled in extra time.
The first period of extra time was a cagey affair as a ten-man Xanthi held on.
But just on 98 minutes Linfield captain Michael Gault volley a superb effort to the corner of the Xanthi net after the Greek side had failed to deal with a Jamie Mulgrew free kick. A top class strike and no more than the home side deserved.
But the game was far from over, on 105 minutes Linfield keeper Jonathan Tuffy pulled off a great save from a Serge Dié free kick. Unfortunately for the blues the rebound fell to the feet of the talented Marcelinho, who finished brilliantly from 12 yards to Tuffy bottom corner for an equaliser on the night and more importantly a two away goal. This again coming totally against the run of play.
As Linfield went chasing the game it was that man Marcelinho who once again shown for the visitors as his mazy run on 110 minutes was halted just on the edge of the area by Billy Joe Burns.
From the resulting free kick for the third time in the evening the impressive Serge Dié went close, this time he was just over the top of Tuffy's crossbar.
With four minutes left Linfield sub Brain McCaul went close with a header from seven yards but it was straight at Xanthi keeper Kyriakidis. Despite a gallant effort it was just not to be for the Blues who now are set to concentrate on domestic action, which kicks off on the tenth of August.
Meanwhile it was also a bad night for Derry city as they crashed out of the same competition, suffering a three-goal defeat at the Brandywell to Turkish side Trabzonspor, 2-7 on aggregate.
Trailing 4-2 from the first leg, Derry's task became virtually impossible when in the 56th minute Mierzejeski's scuffed shot found its way to Paolo Henrique and he bundled into an un-guarded net.
Sen's cross saw Henrique drill home the Turks' second goal on 81 minutes.
And in stoppage time, salt was rubbed into the Derry wounds when Henrique this time turned provider to find substitute Abdulkadir Ozdemir and he completed the rout.