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 pair refused a request from security to leave the venue over their behaviour, the force said.
Counter terrorism police were called to assess the incident but will have no further involvement, with the probe now in the hands of the crime investigation team.
Prime Minister Anthony Albanese praised the officers involved in the search.
"This is pretty shocking reporting, frankly, that two men tried to do this, it is good that they have been charged," he told ABC Radio Sydney.
"Frankly, I hope that they get the book thrown at them for this and I do want to thank Victoria Police for their work in keeping people safe."
AFL Fans Association President Ron Issko was also shocked 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.
"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."
It is unclear how the weapons got into the MCG, which underwent a security upgrade in 2024 including the roll out of artificial intelligence sensors, called Evolve Express.
"Evolv Express uses sensors combined with AI to differentiate between weapons and common metals people carry," according to the company's website.
Both men who have been charged 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 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.
