The Cymru Premier side had a massive challenge in front of them against the Greek side – but like they have done throughout their first ever group phase campaign, they battled resolutely.
A goal in each half from Filip Duricic and Foris Ioannidis was enough to hand the visitors the win, in front of a crowd just shy of 6,000 at Shrewsbury’s Croud Meadow.
But Craig Harrison’s side gave the former European Cup finalists a scare a number of times on the night, with goalkeeper Bartomeij Dragowski called into action on a handful occasions.
Despite the defeat, the two goal scoreline was a positive for the Saints as their goal difference, coupled with their solitary win over Astana still gives the Oswestry side an outside chance of qualifying for the play-off phase.
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It was a mammoth task that faced the Saints against a side who, despite having an off season in the competition, have a huge pedigree on the European stage.
They possessed nine full internationals in their starting line-up and it showed in the early stages, as they began very much on the front foot.
The Saints suffered an early set back as Ash Baker went down with a hamstring injury, forcing Harrison into an early re-think with Josh Daniels coming off the bench.
The gulf in class showed on the quarter hour mark, as Ioannidis’ cross found Filip Duricic, who was denied by a superb save from Connor Roberts.
But seconds later, despite making an initial save from a close range effort, Duricic wasn’t to be denied as he stroked home.
It was starting to look as though it may well be a long evening for the Saints – but they did settle and had three half chances in quick succession.
Ben Clark looped an effort over after Jordan Williams challenged the visiting keeper – before they were twice denied by Bartlomiej Dragowski.
Josh Pask’s glancing header from a corner was kept out by the Polish shot stopper, before Daniels rose to meet a Danny Redmond cross but he was also denied.
They went close yet again on the half hour mark, as Clark’s glancing header from a Ryan Brobbel corner had the goalkeeper scrambling, as it looped just over.
Harrison’s men were banging on the Panathinaikos door but they couldn’t find a way through.
The visitors called Roberts into action twice in the closing stages of the half, but it remained 1-0 at the break and considering the start to the game the Saints would have been happy with the half time situation.
Early in the second period and the Saints were very much having to dig in a ride wave after wave of pressure from the visitors.
And they should have gone further ahead just before the hour mark, as Giorgos Vagiannidis rounded Roberts and had an open goal at his mercy but somehow Daniels launched himself in front of the ball to keep them out.
But the chances were coming and it only felt like a matter of time before a second came along. It did moments later but it was in frustrating fashion.
Harrison McGahey was controversially penalised for an apparent foul in the box and Ioannidis sent Roberts the wrong way from 12 yards.
Like in the first half though, they composed themselves and fired back as Ben Clark had a low drive gathered by Dragowski.
The Greek outfit were having the lions share of possession but 15 minutes from time a Saints break almost saw them get back into the game.
Brobbel found Clark who then set Holden free, but players got back to snuff out the chance, with muted shouts for a penalty as he was clipped by a visiting defender.
Substitute Declan McManus then had a goal bound free kick kept out – with the Saints far from rolling over against the seasoned European side.
And they almost for their just reward for their efforts with the last kick of the game as Sion Bradley’s volley was blocked and cleared.
It was another valiant display, a credible result and it leaves them still in the qualification mix as they take on Celje in the final game next week.
TNS: Roberts, Baker (Daniels 11), McGahey, Pask, Davies, Redmond, D Williams (Smith 63), Clark (Wilson 78), Brobbel (Bradley 78), J Williams (McManus 63), Holden
Subs not used: Edwards, Marshall, Bodenham, Cieslewicz, Bradley, Canavan, Wilson, Woollam, Doforo