The Australian Olympic Committee confirmed on Monday (AEST) that the passports had been returned, marking the end of the saga which had left the athletes departure date uncertain.
The nine — cyclists Ashlee Ankudinoff and Melissa Hoskins, rugby sevens player Ed Jenkins, archers Alec Potts and Ryan Tyack, rowers Olympia Aldersey, Fiona Albert and Lucy Stephens, and hockey player Simon Orchard — were charged with falsifying a document.
They were fined 10,000 reais (about $4,100) each and placed on a two-year good behaviour bond after being held by police for 10 hours throughout Friday night and into Saturday morning.
A public holiday in Rio on Monday had meant the Australian Olympic Committee would not be able to pay the fine and collect the athletes' confiscated passports unless they could do so outside the city.
Australia's team is due to leave Rio on a chartered flight on Monday night but the nine athletes were in line to be left behind until a second flight on Tuesday.
Earlier, Australian chef de mission Kitty Chiller said the athletes did not yet have their passports.
"It is a public holiday in Rio tomorrow and it is actually physically not possible to have the fine paid and passports delivered tomorrow," Chiller said on Sunday.
"Our latest understanding is that we will need to drive out of Rio to make the payment and collect the passports. We will do everything we can to get the passports back."
It's not their fault, says Chiller
The athletes knew they were using tampered accreditations but Chiller said it was not their fault. She has personally apologised to the athletes.
"It was a very difficult night for them and it shouldn't have come to that," she said.
Chiller said tampering with accreditations to get into venues was widespread.
"It's been a practice that's happened in many Olympic Games and amongst many NOCs," she said.
"I became aware of it a few days earlier and I put a stop to it. I said that's not the way that our team should behave and it shouldn't be facilitated that that practice was put in place."
Chiller said the athletes understood they might have to stay in Rio until Tuesday.
Asked on Saturday how it could not be the fault of the athletes, Chiller replied: "We will complete our own internal investigation about how the circumstances arose that the athletes arrived in the venue with accreditations with a different access code to their own".
Chiller gave a similar answer when asked if there were other people involved in the tampering.
AOC chief executive Fiona de Jong, a lawyer, helped strike a deal with a Rio judge which ensured the athletes avoided conviction and a potential five-year jail term.
Palmer free to leave Rio
Swimmer Josh Palmer will be free to join the Monday flight after being interviewed by Rio police for nearly six hours on Saturday over his claims he was robbed at gunpoint in Copacabana.
Palmer was called in by police after initially refusing to take official action over his claims an armed man had forced him to withdraw $1,000 from an ATM in Copacabana.
An Australian Olympic official said police accepted his version of events and no further action will be taken.