The governing body confirmed that security had been acting within the rules at the time, with the shirt initially considered ‘too political’.
However, in a swift reversal, officials acknowledged the broader context surrounding Khan’s situation.
‘Given the widespread concern in the cricket community for Imran Khan’s welfare, we believe this is a humanitarian issue and we will act accordingly,’ a Cricket Australia spokesperson said.
The updated stance meant spectators would be permitted to display messages of support for Khan for the remainder of the match.
Brown was later spotted inside Junction Oval wearing the shirt.
Khan, 73, has been imprisoned since 2023 after being charged with corruption, allegations he denies. He was hospitalised last month due to an eye condition before being returned to jail.
His situation has drawn global concern, with more than a dozen former international captains signing a letter urging authorities to ensure his health and safety.
The controversy unfolded alongside a disrupted start to the Sheffield Shield final itself, with rain heavily impacting play across the opening days.
Play resumed on day three following a 50-minute rain delay, with Victoria restarting at 4-110.
The ladder leaders remain under pressure, trailing South Australia by 88 runs as their first innings continues.