The Magpies fell behind to Denis Epstein's early strike before a brilliant free-kick from Ryan Taylor ensured Pardew's men took an away goal advantage back to the Sports Direct Arena.
And the 51-year-old went on to express his belief that his side should now go on to qualify, but admitted disappointment that the tie was not wrapped up in Greece.
|ALL THE WAY?
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"In the second half, I was a little bit disappointed we didn't get the win - I thought there were good opportunities - but overall, I was very, very pleased with the performance.
"They [Atromitos] have shown us tonight that it's not going to be a pushover and it's not going to be a foregone conclusion, so we have got to be right and we have got to make sure that the team is strong enough.”
Pardew made nine changes from the side which beat Tottenham on Saturday, including bringing in goalscorer Taylor, but he admitted that the Englishman may still not have done enough to earn a first-team berth against Chelsea at the weekend.
Pardew said: "I should think in the Premier League, there are not too many players at dead balls who have the accuracy of Ryan.
"He is desperate to play in the first team, but he has got some good performances from Saturday's game against Tottenham in front of him, so he has got to be patient.
"When he gets his chance, what more can he do? He played very well - and hopefully there are a few more of those, please."