The star left-hander was spotted at training on Tuesday with the words "all lives are equal" and "freedom is a human right" written across his boots.
But the ICC stepped in on the eve of Australia's first Test against Pakistan, with Khawaja risking personal and team punishment if the messages were visible during a match.
However, Khawaja did instead wear a black armband when he walked out to bat to show solidarity and respect for those suffering during ongoing conflict in the Middle East.
After releasing a powerful video to social media on Wednesday night, Khawaja expressed his "frustration" about the situation ahead of play during two interviews on Thursday.
All Lives are Equal. Freedom is a Human right. I'm raising my voice for human rights. For a humanitarian appeal. If you see it any other way. That's on you... — Usman Khawaja (@Uz_Khawaja) pic.twitter.com/8eaPnBfUEbDecember 13, 2023
"There's so much that has happened in the past that sets a precedent," he told Fox Cricket.
"I'm in full support of Black Lives Matter. There's plenty of guys who have written on their shoes before.
"There's other guys that have written religious things on their equipment, and under the ICC guidelines, that's not technically allowed, but the ICC never says anything on that.
"I find it a little bit disappointing they came down hard on me and they don't always come down hard on everyone else."
Khawaja reiterated he intends to challenge the ICC rules "as soon as possible" after tapping over the messages on his shoes for this match.
The first Muslim to represent Australia in international cricket, Khawaja has been left deeply affected by events in the Middle East.
His stand comes as Israel's military push into Palestine continues to spread, causing devastation among civilians living there and creating a humanitarian crisis.
Usman Khawaja conducts an interview before the start of the opening Test against Pakistan. (Richard Wainwright/AAP PHOTOS)
The 36-year-old conceded not everyone was ever going to agree with his views but had found some of the commentary "distasteful" and he had felt "uneasy".
"I am a grown man; I can do anything I want, but I think the ICC will keep coming down and giving me fines and at some point it will detract from the game," Khawaja told the Seven Network.
"I stand by what I said, I will stand by that, I think forever.
"For me, I need to get out there and concentrate on what I am doing but it is right at the forefront of my mind."
Australia captain Pat Cummins supported Khawaja's stance.
"You want everyone to bring their own individual self to the team. And what was on the shoes - all lives are equal - I mean, I support that," Cummins said on Thursday.
"I think that's not very divisive. I don't think anyone can really have too many complaints about that."
