The north Londoners had come into the Group F encounter hoping for the victory that would see them progress to the knockout stages for the 12th successive season, although a mixture of resolute defending and poor finishing put paid to that.
Arsenal looked weary from the exertions of Saturday's 5-3 victory at Chelsea and lacked the cutting edge brought by talisman Robin van Persie, who started on the bench against the French outfit.
While the home side were frustrated at their inability to emulate last month's win at the Stade Velodrome, a point was the least Marseille deserved from a plucky performance.
Didier Deschamps' side started with a free-flowing attacking formation in which brothers Andre and Jordan Ayew shone, especially in a first half they dominated for the most part.
Arsenal managed to keep the visitors at bay but the majority of the 59,961 crowd at the Emirates Stadium were sent home disappointed, with a Van Persie chip the only opportunity of note in a poor second period.
Heading into the clash, Arsene Wenger made two changes to the side that beat Chelsea at the weekend.
Johan Djourou and captain Van Persie were dropped to the bench, with Carl Jenkinson and Park Ju-young coming in in their place.
Marseille also made two changes to their starting line-up, bringing in Mathieu Valbuena and Alou Diarra.
The pair's inclusion was part of an attack-minded philosophy adopted by OM at the Emirates Stadium and one that almost paid dividends immediately.
Andre Ayew jinked down the left flank and fired in a low cross that his brother, Jordan, almost flicked home within the opening minutes.
Marseille continued to dominate the opening exchanges as the Ayew brothers dazzled Arsenal's backline, with Andre poking just wide after some neat interplay in the fifth minute.
Loic Remy was the architect of that opportunity and he saw a goalbound shot blocked moments later, before Theo Walcott was denied by a sprawling Steve Mandanda save at the other end.
Gervinho was next to test Marseille captain Mandanda, before a deep cross by Andre Santos was almost converted at the back post by Aaron Ramsey.
Arsenal were now controlling play and defending deep, aware of the threat Marseille posed on the counter-attack.
But despite the home side's best efforts, OM were still finding space in the attacking third and Remy came close with a low drive after a neat one-two with Benoit Cheyrou.
Wenger's side were also looking dangerous on the break and, after Gervinho saw a drive stopped superbly by Mandanda, hesitation saw Park and then Ramsey waste decent opportunities to score.
Diarra was booked for a foul on the latter as Marseille struggled to keep the Arsenal attack at bay, with the resulting free-kick curled just wide by Mikel Arteta.
The second period started in the same manner in which the opening 45 minutes ended, with Arsenal dominating possession but failing to create any clear chances.
Gervinho and Park were both struggling to produce the moment of magic that would force an equaliser, which led Wenger to replace the latter with talisman Van Persie in the 62nd minute.
The Holland international received a standing ovation from the home faithful on his introduction, as did Ramsey when he was taken off in favour of Tomas Rosicky moments later.
Arsenal looked to be struggling after their weekend exertions at Stamford Bridge as the match petered out into a tepid affair.
Neither side showed any cutting edge and the match seemed set for a draw, leading Wenger to make his last roll of the dice with the out-of-sorts Gervinho replaced by Andrey Arshavin.
Moments later, out of nothing, Van Persie wriggled free only to waste the best opportunity of the half. The Arsenal skipper was released by an exquisite through-ball from Rosicky, although his audacious chip was thwarted with ease by Mandanda.
It was to be the Gunners' only chance of note as the clock ran down and OM pressed for the all-important goal.
After Jordan Ayew's header flew wide, substitute Morgan Amalfitano shot across the face of goal before then seeing a cross blocked by Per Mertesacker.