Newcastle 1-0 Atromitos (2-1)
Haris Vuckic's long-range goal helped Newcastle beat Atromitos to reach the Europa League group stages.
Newcastle lost their goalscorer from the first leg, Ryan Taylor, to a serious-looking knee injury early on.
But his replacement, Vuckic, struck a diagonal shot for his first Newcastle goal to earn the lead after 21 minutes.
Tim Krul was fortunate to stay on the pitch after he brought down Chumbinho in the penalty box and Elini Dimoutsos wasted a late chance as he fired wide.
Denis Epstein also shot over as the Greek side finished strongly, but overall Newcastle enjoyed a relatively comfortable night as they qualified for the next round on their first European foray in more than five years.
Alan Pardew's side will face far sterner tests in this competition, but there were encouraging performances from Gabriel Obertan and Sylvain Marveaux on either wing.
The pair caused havoc down the flanks and were one of seven changes made to the team following Newcastle's defeat at Chelsea, with Marveaux testing Atromitos keeper Charles Itandje early on after James Perch curled wide.
Vuckic's introduction on 11 minutes came after Taylor was injured by skipping over a challenge and then collapsing as his knee seemed to give way.
It looked like it could be a grave problem, but 20-year-old Vuckic wasted little time in putting Newcastle in front when he collected Danny Simpson's throw-in from the right, moved inside and lashed a shot into the bottom corner via a deflection off Matias Iglesias.
The Slovenian substitute could have added another, but despite the hosts holding the upper hand in the first half, Brazilian Chumbinho caused several moments of concern.
First, his shot was saved by Krul and then the Newcastle keeper evaded a red card and a penalty in the same moment when he brought down the Brazilian after he fumbled Denis Epstein's shot.
The referee decided to book the Atromitos forward instead.
Newcastle looked comfortable to begin with after the break and Obertan could have doubled the lead on the night, as former Liverpool keeper Itandje parried his firm shot.
But as the time ticked away, the visitors grew more dangerous and they missed a golden chance when Iglesias's shot was deflected into the path of Dimoutsos, but he blazed wide of the post from an angle about 10 yards out.
Newcastle boss Alan Pardew: "It looks like Ryan Taylor has picked up a bad knock, and I might now have to speak to the chairman because we might need to bring someone in on the back of that. Let's hope it's not as bad as we fear."