For Juergen Klopp's team, the win in France and qualification for the knockout stages was a huge morale-boosting result after a shaky start to the season.
Having dropped to third in the Bundesliga after losing to rivals Bayern Munich, talk of a first crisis for the 2011 and 2012 league champions quickly surfaced.
But despite a string of absentees, Dortmund battled on to win their last two Group F games in Europe to book a spot in the next round by the slimmest of margins after they finished level on 12 points with Arsenal and Napoli.
They left it late on Wednesday, with home-grown talent Kevin Grosskreutz netting the winner that saw them through three minutes from time as group winners courtesy of a better head-to-head record.
"The game had a Malaga-style intensity," Klopp was quick to admit in reference to last season's quarter-final win over the Spaniards when they scored two goals in stoppage time in yet another dramatic European encounter.
"My boys played their hearts out and were concentrated to the limit, even though there was pressure after Napoli took the lead (against Arsenal)."
Dortmund, whose stunning run to last year's final before losing to Bundesliga rivals Bayern, looked to be on their way out a few weeks ago after losing at home to Arsenal.
Facing an early exit before Christmas was not in their plans and the team, without defenders Mats Hummels, Neven Sobict, midfielder Ilkay Guendogan and a string of others, bounced back in style beating Napoli 3-1 to set up a crunch match against Marseille.
With group rivals Napoli beating Arsenal, Dortmund needed to win in France to secure a round of 16 spot at the expense of the Italians.
Klopp had to dig deep into his squad to field a starting lineup, deploying 18-year-old rookie Marjan Sarr who has yet to make his Bundesliga debut.
The gamble paid off, leaving Dortmund, one of a record four German teams that qualified for the knockout stages, wanting more from a tournament they won for the only time in 1997.
"To celebrate with our fans after the game is the best feeling," said Grosskreutz. "To come from third in the group and top it in the end is fantastic. Now we are through and want to keep winning in the competition."
With some of the injured players expected to be back fit when the Champions League restarts in February, fans can take a breather before more Dortmund drama next year.