The result means Arsenal finish top of Group F ensuring they will avoid the majority of tricky knockout ties.
Samuel Bastien and Selim Amallah had the hosts up by two goals with 21 minutes remaining.
On finishing top of the group, caretaker boss Freddie Ljungberg said: "Of course, it's very very good.
"We started [the group] really well and then we had some problems in two games and then we came to this.
"We have played a lot of games lately and of course I wanted to give the young ones a chances, but I also needed to rotate because we have injuries in the West Ham game and I didn't have many options left.
"We have a game again on Sunday, so of of course it was a little gamble but I believe in those players and we pulled through and are top of the group."