Khawaja had hoped to use images of a dove holding an olive branch, as well as a reference to article one of the Universal Declaration of Human Rights, on one of his boots and bat in the Boxing Day Test against Pakistan.
It comes after the 37-year-old was charged by the International Cricket Council (ICC) for wearing a black armband during the first Test in Perth.
Before that match, Khawaja wrote on his boots "All lives are equal" and "Freedom is a human right".
But Khawaja was warned against displaying those messages, and he taped over his shoes before play.
Khawaja and Cricket Australia (CA) had been working with the ICC during the past week to find a way for the left-hander to show his support without being "divisive".
Michael Hussey chats with Usman Khawaja at training ahead of a Test against Sri Lanka in 2013. (AP PHOTO)
Hussey, who played with Khawaja for Australia and at the Sydney Thunder, believes his former teammate is simply confident in himself in the later stage of his career to voice his opinions.
"I think his real authentic self is coming out - this is who Uzzy is," Hussey said on Monday after being confirmed he would be inducted into the Australian Cricket Hall of Fame.
"He's very passionate in his beliefs, his morals and his values and he's not afraid to put them out there.
"I'm quite proud of him actually.
"I don't think he's trying to be divisive or political or anything like that ... I respect what he's done.
"He's got to follow the rules set by the ICC, but he certainly is sticking true to what he believes in."
Khawaja has called out inconsistency from the ICC with how the governing board enforces its own rules.
On Monday, the 67-Test veteran uploaded a post of other international cricketers displaying messages on their bats.
View this post on Instagram A post shared by Usman Khawaja (@usman_khawajy)
"Sometimes you just gotta laugh. Cya at Boxing Day! #inconsistent #doublestandards," Khawaja posted on Instagram, with the Kanye West song 'Can't Tell Me Nothing'.
CA chief executive Nick Hockley had supported Khawaja with his application to the ICC.
"Over the last week or so we've been working really constructively with Uz, really to find a way that again is non-partisan," he said on Tuesday.
"The symbol of the dove is an universally recognised symbol of peace.
"That being said, the ICC have got their rules and think they explained their rationale really clearly and we respect that.
"What we've been really clear about is that we support Uzzy and and all our players really to share what the what they believe over their own channels."
Australia captain Pat Cummins on Monday described the dove symbol as "pretty vanilla" and said it was "not really" any different to observant Christian Marnus Labuschagne's eagle, which represents a Bible verse.
