A sticker showing a black dove and the words 01:UDHR - a reference to Article One of the Universal Declaration of Human Rights - was on his bat and shoes during training in Melbourne on Sunday.
The star batter had multiple meetings with Cricket Australia over recent days to find a message that would be appropriate for the second Test this week, local media said.
But his latest humanitarian gesture has been turned down by the International Cricket Council, The Australian and Melbourne Age newspapers reported.
The ICC were not immediately available for comment.
Khawaja, a Muslim, was stopped from wearing shoes emblazoned with the hand-written slogans 'Freedom is a human right' and 'All lives are equal' during the first Test in Perth. He had wanted to show his support for the people of Gaza.
But he was told they flouted ICC rules on messages that relate to politics, religion or race.
He wore a black armband during the match and was reprimanded by the ICC, but insisted afterwards it was for a "personal bereavement" and vowed to contest the ruling.
Khawaja spoke on Friday about how the Israel-Hamas conflict had affected him, saying he despaired at seeing how many children had been killed.
"When I'm looking at my Instagram and seeing innocent kids, videos of them dying, passing away, that's what hit me the hardest," he said.
"I don't have any agendas other than trying to shine a light on what I feel really passionately, really strongly about."
