The Magpies came from behind to earn a valuable draw as Ryan Taylor responded to Denis Epstein's opener with a superb free-kick and put the Group Stages within sight
Alan Pardew's men had fallen behind midway through the the first half when winger Denis Epstein hit home from close range. However, Taylor levelled matters just before the interval with a superb free-kick from 20 yards out to give the Magpies the all important away goal.
Newcastle with one eye on Saturday evening's Premier League clash with Chelsea, made eight changes from the side that beat Tottenham last weekend, with Steve Harper, James Tavernier, Taylor, Gael Bigirimana, Vurnon Anita, Gabriel Obertan, Dan Gosling and Sylvain Marveaux all coming into the starting eleven.
The contest took a while to spark into life, but Newcastle did have a chance to take the lead 20 minutes in when Atromitos keeper Charles Itandje failed to handle a deep cross from Tavernier, but the Atromitos defence cleared the danger before Cisse was able to pounce.
However, it was the Greek side who poked their noses in front minutes later when Epstein, who had beaten Tavernier down the left-hand side on a number of occasions earlier in the half, latched on to a high through ball from Nikola Beljic to slot past Harper from close range.
Pardew's side responded well as they began to dominate possession, and they came close to equalising when Taylor curled a free-kick towards goal, only to be denied by an unconvincing save from Itandje.
The game looked to be meandering towards the interval, but on the stroke of half time the Magpies did level when Taylor curled a free-kick into the bottom corner afte Gosling had been fouled on the edge of the area to delight the small army of travelling Newcastle supporters.
Newcastle started the second half quickly and could have snatched the lead just minutes into the period when Gosling nodded Cisse's deflected right-wing cross straight at Itandje.
The visitors continued to grow as the second half developed, and they were denied by Itandje again just before the hour mark, the Frenchman producing a superb save from Obertan's driven effort after Taylor's inswinging free-kick had been knocked into his path by Williamson.
Despite pulling off that fine save, the Atromitos' stopper looked uncomfortable under the high ball and he nearly handed the Magpies the lead when he flapped at a lofted cross from Obertan. However, the former Liverpool man just managed to wrestle the loose ball away from Cisse before the Senegalese international had a chance to pull the trigger.
Atromitos laboured to try and re-take the lead, but again it was the visitors who should have hit the front when Obertan broke free down the right hand side before squaring a ball into Cisse. The striker's clever flick on found substitute Romain Amalfitano but he failed to get his shot away when through on goal as Itandje reacted well to snatch the ball from his feet.
The game began to die down as both teams tired in the closing stages, but there was a moment of history when 17-year-old forward Adam Campbell replaced Cisse to become the youngest player to ever compete a European competition for the Magpies.
Newcastle did create a number of chances late on, but they were unable to break down a determined Atromitos defence, and were left to settle for a draw ahead of next week's return leg at the Sports Direct Arena.