The game looked to be heading towards a stalemate as both sides struggled to find the net throughout the 90 minutes.
However, with just seconds left the 17-year-old was played behind the Gunners defence and poked the ball past Dejan Iliev to give the hosts the win.
Arsenal started the stronger of the two sides and should have taken the lead in the 14thminute when Nicolas Yennaris won the ball in midfielder and played Nigel Neita through on goal but the striker could only fire his effort over the bar.
Anthony Jeffrey gave Chuba Akpom a great chance to put the visitors in the lead again but the 17-year-old could only volley over from inside the area after the midfielder had done well to create the opening on the left.
The Gunners almost paid for the lack potency in front of goal as Emanuel Loiacono curled a delightful free-kick towards the top-corner from 35-yards but Iliev was on hand to make a good save parrying the ball to safety.
Marseille midfielder Billal Omrani nearly broke the deadlock early in the second-half but his free-kick went just inches past. Minutes later Jeffery responded for the Gunners but he saw his low-shot from inside the penalty area stopped on the line.
The home side though they had taken the lead four minutes from time Iliev headed the ball straight to Marcellin Anani but he was flagged offside as he slotted the ball into the net.
Arsenal didn’t heed this warning and the hosts finally got their goal in the last minute as a pass from the midfield was threaded through the Gunners defence and Kisaku latched onto the ball and made no mistake firing past Iliev.