The athletes were charged with using false documents, Rio de Janeiro Civil Police said during a news conference Saturday.
After appearing in front of a judge in the early hours of the morning, the athletes were released with a two-year good-behavior bond and ordered to pay the fines.
The Australians' passports have been seized until they pay the fine.
Speaking to reporters on Saturday, Australian Chef de Mission Kitty Chiller said the Australian athletes were not at fault for the problem.
"(I am) very disappointed that our athletes had to go through what they did go through last night," she said. "I think it's very important to note that the athletes were definitely not at fault. We have and will continue to provide as much support and counseling to them and their parents."
She said Australia has started an internal investigation into how the accreditation was tampered with.
"It's unfortunately a practice that has been traditional not only in Australia but in other countries as well for many Olympic Games of putting a sticker on your accreditation with another venue access code on it," Chiller said.
Deputy Chef de Mission, Fiona de Jong, apologized to the court and explained that the athletes were supporting their teammates, they were not attempting to defraud anyone, no one had suffered a material loss and no one was harmed as a result of the incident, the Australian Olympic team said in a statement.
The Australian athletes' fellow basketball players also suffered a disappointing night -- losing to Serbia 61-87.
The Serbian team will face Team USA in the final.
It's not the first time Australian athletes have had a run-in with officials at Rio 2016.
Night out ends in mugging
After a big night out in Copacabana, Australian swimmers Josh Palmer and Emma McKeon not only failed to return to the Olympic Village in good time -- but were banned from attending the Games' closing ceremony
by team management.
McKeon stayed out at a nightclub until the early hours of the morning, while Palmer headed to a beach kiosk with a friend to continue drinking.
Once Palmer's friend had left, a man approached him and forced him to withdraw $1,000 cash from a nearby ATM, the swimmer told officials.
He was later found by two businessmen who reported the Australian was disoriented and had lost his wallet and phone.
As well as not taking part in Monday's closing ceremony, Palmer and McKeon are prohibited from leaving the Olympic Village between the hours of 8 p.m. and 8 a.m. Swimming team management also imposed a 2 a.m. curfew on all team members for the rest of the Games.
Chinese drug cheat claims
Australian swimmer Mack Horton called China's Sun Yang a "drug cheat"
-- before going on to beat him in the 400m freestyle.
Gold medalist Horton beat silver medalist Sun by a mere .16 of a second, describing his win as one "for the good guys."
Sun served a three-month ban for testing positive for a banned substance in 2014.
The Australian's comments sparked fury in China after an emotional Sun broke down in the post-race news conference, accusing Horton of deliberately trying to psych him out.
But Australia's chef de mission Kitty Chiller flatly ruled out any chance of an apology, telling reporters that Horton "has every right to express his views and his displeasure."
Athletes' Village safety fears
The Australian delegation initially refused to move into the athletes' village
amid safety concerns, instead opting to stay in a hotel.
"Problems include blocked toilets, leaking pipes, exposed wiring, darkened stairwells where no lighting has been installed and dirty floors in need of a massive clean," Chiller said.
"In operations areas water has come through the ceiling resulting in large puddles on the floor around cabling and wiring."
Rio de Janeiro Mayor Eduardo Paes later offered to get a kangaroo for the team to help them "feel at home here."
Responding to Paes' offer, Australian committee spokesman Mike Tancred told a Brazilian newspaper "we do not need kangaroos, we need plumbers to account for the many puddles found in the apartments."
The team eventually moved back to the village three days after the official opening.