England midfielder Wilshere showed no signs of any fatigue as he swept the Premier League leaders ahead after just 28 seconds.
Although club-record signing Mesut Ozil missed a first-half penalty, another close-range effort from Wilshere made sure of victory to keep the Gunners top of Group F.
A draw on matchday six away to Napoli, who lost 3-1 at Borussia Dortmund on Tuesday, will now see Arsene Wenger's men qualify in first place and seeded for the last 16.
Arsenal had swept into the lead after just 28 seconds when Wilshere broke clear and cut back inside to smash the ball past Steve Mandanda.
The Marseille goalkeeper then saved from Aaron Ramsey at point-blank range, but Arsenal should have been further ahead just before the break when Ozil's weak penalty was palmed away.
Eventually, Arsenal's pressure in the second half told when Wilshere swept home Ozil's pass on 65 minutes.
Marseille - who had lost all four European ties so far - did mount a brief rally.
Substitute Florian Thauvin collected a pass at the edge of the penalty area and drove a shot goalwards, which parried up off the legs of goalkeeper Wojciech Szczesny and the ball looped towards the empty net - but full-back Nacho Monreal, in for the ill Kieran Gibbs, recovered to clear off the line.
Szczesny needed to be alert again to get down at his near post to save well from Florian, once on the watchlist of Gunners boss Wenger.
Arsenal substitiute's Santi Cazorla blazed over from 10 yards and then Theo Walcott stabbed wide when clear through, but the result was already secure - leaving the Gunners on the brink of the last 16 in Europe's elite club competition once again.
Arsenal were looking to build on their impressive win in Dortmund earlier this month, and got off to a flying start.
Bacary Sagna released Wilshere down the right. The England midfielder took the ball on into the penalty area, before cutting back inside his marker to curl a superb left-footed shot past Mandanda and into the top corner.
Arsenal cut Marseille open again on six minutes, as Olivier Giroud slipped Wilshere inside the full-back.
This time the England man did look to pull the ball across the face of goal where Ramsey arrived on cue in the six-yard box, only for Mandanda to make a superb reaction save at point-blank range.
Marseille slowly managed to stem the tide and saw a spell of posession in midfield.
Ozil's first touch was heavy after being picked out in the penalty area by a chipped pass from Ramsey - which was a sign of the current inconsistencies for the £43million Germany playmaker.
It did not get any better for the former Real Madrid man when he had the chance to score from the penalty spot on 37 minutes after Nicolas N'Koulou tripped Ramsey, although the challenge looked just outside the left side of the box.
However, after taking an age with his one-step run-up, Ozil clipped the ball to the left and Mandanda made a smart save.
Ozil was then upended by Jeremy Morel as he darted down the middle, but Ramsey's 20-yard free-kick was fired straight into the wall.
Arsenal started the second half with some purpose.
Ozil's precision pass set Giroud free, and his shot was deflected just wide.
The German then collected a pass from Wilshere on his chest and drove in an angled shot which was saved by the Marseille keeper.
It was finally 2-0 on 65 minutes.
Ramsey's pass found Ozil in the right side of the penalty area and his cutback through the six-yard box fell perfectly for Wilshere, who drove the ball past Mandanda.
Arsenal, though, allowed their tempo to drop, and it almost allowed the French side back into the tie.
Marseille couldn't find a way back however and Arsenal held on to secure a precious win.