Theo Walcott volleyed home in the 65th minute after benefiting from Jeremy Morel's defensive blunder before Aaron Ramsey put the result beyond doubt seven minutes from time with a deflected low shot.
Arsene Wenger's side, who looked listless in the first half, are level in Group F with Napoli, who beat last season's runners-up Borussia Dortmund 2-1.
Olympique Marseille had a handful of chances with Andre-Pierre Gignac, Andre Ayew and Rod Fanni coming close to scoringe before Jordan Ayew reduced the arrears with a penalty in added time.
Elie Baup's side, who were eager to make the most of their home games in a tricky group, pressed high and were the first in action when Gignac latched on to Morel's cross after two minutes in a fast-paced opening.
Arsenal dominated possession early on but were lacked penetration up front. The visitors' best chance came in the 10th when Walcott's crossed shot was easily blocked by Steve Mandanda.
Andre Ayew's header shaved Wojciech Szczesny's right post midway through the first half before Gignac sent another header just over the bar shortly before the break.
The hosts came close again early in the second half, but Rod Fanni's fine volley on the turn went narrowly wide.
Arsenal finally came to life in the 54th minute, with Kieran Gibbs's sudden rising shot blocked by Mandanda, who parried Jack Wilshere's half volley four minutes later.
In a moment of panic, Per Mertesacker sliced a clearance over Szczesny but Gibbs cleared the ball off his goal line, denying Gignac who was about to head home an easy goal.
Morel's fluffed clearance of Gibbs's cross ended up in the path of the unmarked Walcott, who fired home with a fine volley from close range to open the scoring.
Ramsey ended Marseille's hopes in the 83rd minute when his low shot from just outside the box took a slight deflection off a defender to go past Mandanda.
Jordan Ayew pulled one back from the spot after his brother Andre was brought down by Ramsey.
Arsenal next take on Napoli at home while Olympique Marseille travel to Borussia Dortmund.
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