The Swiss midfielder was taken off during the Gunners' draw with Crystal Palace on Sunday and his departure was greeted with delight.
Owen believes Xhaka's reaction was wrong but was disappointed to see him booed in the first place.
He tweeted: "About time somebody went against the grain.
"Is Xhaka a great player? No.
"Should he react like that? No.
"But if 60,000 fans boo you off? Where's the unity?
"Expect him to die for the shirt one minute then walk off to a cauldron of hatred the next? #DoubleStandards."