Magnussen, Matt Targett, Eamon Sullivan, James Roberts, Cameron McEvoy and Tommaso D'Orsogna admitted in February they had used the sedative and been involved in "childish" and "stupid" pranks at their training camp in Manchester before the Games last year.
Stilnox, a brand of the medication zolpidem, is not banned by the World Anti-Doping Agency but was prohibited by the Australian Olympic Committee because of its hallucinatory effects and after former Olympic champion Grant Hackett said he had become addicted to it.
A Swimming Australia integrity panel conducted an investigation and found the group had "failed to demonstrate the level of conduct required of members of the team".
"As a result of the Swimming Australia Integrity Panel report, six athletes will be required to make payments to Swimming Australia and will receive deferred suspensions for breaches of their behavioural obligations," the statement added.
The organisation did not specify how much the swimmers would have to pay, or how long they would remain on probation.
Calls to Swimming Australia were not immediately returned.
The investigation report would now be handed to the Australian Olympic Committee for review.
"We believe these athletes showed poor judgement in their actions and behaviour, and such behaviour is unacceptable for members of the Australian swim team," Swimming Australia president Barclay Nettlefold said.
"We have taken many steps towards developing a more positive culture within the team and the organisation already this year, and were confident we are heading in the right direction."
Magnussen was hot favourite to win the 100 freestyle in London, but came away with the silver, while the relay team were had also been tipped for gold but finished out of the medals as Australia slipped to their worst performance in the Olympic pool for 20 years.
- Sports & Recreation
- Australian Olympic Committee
- Swimming Australia