The Switzerland midfielder appeared to tell supporters to "f**k off" as he was jeered while being substituted during Sunday's 2-2 Premier League draw with Crystal Palace.
That promoted even more fury among the Gunners' faithful but Xhaka has moved to explain his actions.
"My feeling of not being understood by fans, and repeated abusive comments at matches and in social media over the last weeks and months have hurt me deeply," he wrote on Instagram.
"People have said things like 'We will break your legs', 'Kill your wife' and 'Wish that your daughter gets cancer'.
"That has stirred me up and I reached boiling point when I felt the rejection in the stadium on Sunday."
Manager Unai Emery on Tuesday refused to discuss Xhaka's position as captain and he was rested for the Carabao Cup defeat to Liverpool.
In a lengthy post by way of explanation he did not offer a direct apology for his actions, only saying sorry if people felt he had been disrespectful.
"In this situation I let myself get carried away and reacted in a way that disrespected the group of fans that support our club, our team and myself with positive energy," added the 27-year-old.
"That has not been my intention and I'm sorry if that's what people thought.
"My wish is to get back to a place of mutual respect, remembering why we fell in love with this game in the first place. Let's move forward positively together."