The midfielder came off the bench to seal victory for the English Premier League side at the Karaiskakis Stadium
Arsenal manager Mikel Arteta hailed the impact of Mohamed Elneny and the rest of the substitutes following their 3-1 over Olympiacos on Thursday evening.
The Gunners took the lead in the 34th minute when Martin Odegaard’s beauty beat goalkeeper Jose Sa.
In the 58th minute, Morocco international Youssef El Arabi levelled matters for the Greek Super League side, before the English team took the lead with 10 minutes left to play courtesy of Gabriel.
A short corner was taken by Willian, who floated the ball to the back post where Gabriel charged in to glance a terrific header across goal and into the far corner.
Elneny – an 81st minute substitute for Willian - settled the encounter with five minutes left to play against Pedro Martins’ men.
And the Spaniard, whose team are unbeaten in their last four games in all competitions, said the Egypt international, along with fellow replacements Daniel Ceballos, Emile Smith-Rowe, Nicolas Pepe and Alexandre Lacazette, were crucial to his side's success against Pedro Martins’ side.
“I don't know, there is still another game to play in this competition and with this level of opponent, anything can happen,” Arteta told club website.
“So, we have to be very prepared to take the game nil-nil and go and win it at the Emirates. Then we will be through.
“With Mo in particular and with the subs, I'm extremely delighted because I know how much they want to play and they are key in this competition.
“If you want to be successful, you need your subs to make an impact and they've done it tonight again.
“And Mo in particular, because of how he's been training so hard to improve his shooting range with Roundy [Steve Round] and he got his reward tonight. It's very important for the team.”
Arsenal take a two-goal lead and three away goals into the reverse fixture leg billed for the Emirates Stadium.
Olympiacos try Larissa for size in their last league game of the season next, while the Gunners welcome Jose Mourinho’s Tottenham Hotspur in the north London derby as they return to English division action.