The men, aged 21 and 25, were arrested on Friday after an operation by Australian Federal Police, alongside investigators in multiple states, led to what is believed to be Australia's biggest ever cocaine bust.
AFP officers raided a property in Londonderry, in northwest Sydney, on Friday as part of a taskforce investigating a drug ring along the country's east coast.
While searching the property, police allegedly located 2.7 tonnes of cocaine in plastic tubs underneath shipping containers.
The tubs were buried in underground bunkers concealed by false container floors, the AFP said.
The estimated street value of the cocaine is $816 million and is equivalent to roughly three million street level deals.
Both men allegedly tried to run away when police arrived but were caught and subsequently charged with possessing a commercial quantity of an illegal drug.
The maximum penalty is life imprisonment.
The men were refused bail on Saturday and are expected to face Penrith Local Court on August 13.
"This alleged plot to distribute nearly three tonnes of cocaine ... demonstrates how highly organised and determined these criminal networks are," AFP Commander Stephen Jay said.
"We will work ... to identify the criminal syndicates and anyone else involved in facilitating this alleged attempted drug import."
The mammoth Sydney discovery is the standout find for investigators under Operation Minjiang, a joint taskforce headquartered in Queensland.
Since starting in May, the operation has seized 178kg of cocaine and 142kg of methamphetamine, bringing the total amount of drugs now seized to more than three tonnes.
Police allege the cocaine seized on Friday was imported into Australia near Midge Point in North Queensland and transported south under the orders of a Sydney organised crime group.
Queensland Police discovered 40kg of cocaine in the water near the Midge Point boat ramp in May after they received reports of a burned out flatbed truck.
Six people were later charged with varying offences including possessing illicit drugs and dealing with proceeds of crime.
The alleged mother vessel used to import the haul of drugs, MV Wealth, has been detained by authorities in the Solomon Islands for further investigation, the AFP said.
Queensland Police Acting Chief Superintendent Troy Pukallus said he was proud of his officers' tenacity in disrupting a massive organised crime syndicate.
"What began with the actions of Mackay police ... evolved into a sophisticated, multi-agency investigation targeting an organised criminal network," he said.
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