The first half was eventful, despite both teams having little to play for. The visitors created several chances, with Raheem Sterling and Leandro Trossard both coming close.
Girona took a surprise lead through Arnaut Danjuma, but Arsenal equalized with a penalty from Jorginho after Thomas Partey was brought down in the box.
Ethan Nwaneri then scored his first Champions League goal, cutting inside and striking into the bottom corner.
In the second half, Arsenal continued to dominate, with Nwaneri coming close to a second goal.
Mikel Arteta’s men were awarded another penalty in stoppage time, but Sterling’s effort was saved. It proved inconsequential as the Gunners held on for victory to round off an impressive UCL campaign.