Victoria Police said the weapons were found on each of the men during a search about 8.30pm on Thursday, as a crowd of 82,058 fans watched Collingwood defeat Carlton.
Officers were asked to get involved when the men refused a request from security to leave the venue over their behaviour, the force said.
It is unclear how the weapons got into the MCG, which underwent a security upgrade in 2024.
AFL Fans Association President Ron Issko was shocked by the incident and said nothing like this had ever happened.
He said fans were subjected to several security measures including walking past detector pillars and individual security checks.Â
"I'm waiting for the AFL to come back to me to explain what's happened and what they're going to do about it. And if they have to make some changes this weekend to security, fans will accommodate," Mr Issko told AAP.
"We'll just wait for an explanation. But I'll be going to the footy this weekend and I've got all the confidence in the security and the police at the footy."
He said any security upgrades must be done urgently.
"Ninety-nine per cent of fans are great. If we've got some ratbags let's get rid of them," he said.
"Let's not allow them come to football, and let's beef up security if we have to."
Both men were on bail at the time.
A 27-year-old man from Broadmeadows was charged with possessing an unregistered handgun, possessing ammunition without licence, altering the serial number of a firearm, possessing a loaded firearm, possessing a prohibited item (Major Event Act offence) and failing to appear on bail.
A 21-year-old man from Roxburgh Park was charged with being a person prohibited from possessing a firearm, possessing ammunition without licence and committing an indictable offence while on bail.
The men were remanded to appear in the Melbourne Magistrates' Court on Friday.
A spokesperson from the Melbourne Cricket Club, which manages the stadium, said they were unable to comment on the allegations as an active police investigation is under way.
The AFL has been contacted for comment.