It was the most unlikely of qualifications after the North Londoners lost three of their first four games in this season's competition.
But it was the manner of the victory that was striking too.
Arsenal to a man stepped up when it truly mattered and the result could be a major turning point, not just this season, but in the club's history.
That's because the circumstances are eerily similar to that of Premier League rivals Liverpool.
It's an omen
Almost 11 years ago to the day Anfield witnessed one of the most famous nights in its history.
Liverpool, like Arsenal, were staring elimination from the Champions League in the face.
Rafa Benitez's side needed to score three second-half goals against none other than Olympiacos to progress to the knockout stages of Europe's premier competition.
Somehow - and thanks in no small part to Steven Gerrard's most significant strike in a Reds shirt - they managed to win 3-1 and it was a major watershed moment.
We all know what happened next, Liverpool went on to win the Champions League final in Istanbul the following May in remarkable fashion.
But Reds fans always point back to the Olympiacos match as the clincher.
It is a match remembered as fondly for the spirit of the team as it was the significance of the result. In fact supporters even refer to the 'spirit of Olympiakos' today.
Arsenal showed the 'spirit of Olympiacos'
And that same kind of spirit was evident in Arsenal as Giroud this time rather than Gerrard slayed the Greek side with a milestone moment in his career, scoring a fine hat-trick.
If Arsenal do go on and finally lift the Champions League trophy, Gunners fans, like Liverpool's before them, will look back to that night and the spirit of Olympiacos as the catalyst for their success.
Having finished second they will have to do it the hard way, but then again so did Liverpool.