The forward has taken over the armband from the Swiss midfielder following the reaction to the latter's substitution against Crystal Palace last month.
Aubameyang's captain's column called for support for both Xhaka and the rest of the team.
"I took over from Granit in tough circumstances but I am very proud to be wearing the armband," said Aubameyang.
"It is an honour. It comes with a lot of responsibilities but I feel I can do a great job.
"I would like to also say a word for Granit.
"I understand that sometimes one can make mistakes. It happens to all of us. Granit is one of us. We are all here for him and I know how strong he is.
"It was tough to see all of this happening but we need to move forward together.
"This is my message for you Arsenal fans. We need you. You are amazing, your support is amazing and we need to all pull in the same direction.
"I really hope you will be massively behind us today and for the rest of the season."