When customers used their smartphones to check-in, they were instead directed to an anti-vaccination website.
Colin Mark Davies, 51, has been charged with two counts of obstructing operations related to Covid-19.
In Australia, anyone found tampering with Covid-19 QR codes faces arrest and a penalty of up to $10,000 (£5,577).
The country operates a similar system to that of the UK's Test and Trace scheme, which asks customers to check in to venues so they can be notified if they come into close contact with Covid-19.
Mr Davies has since been released on bail on the condition that he does not carry any loose QR labels. He must return to court in July to be sentenced.
His lawyer said he "wanted to get his message out to the public".
Mr Davies has also been charged with possessing a prohibited weapon, after police searched his home and found a doubled-sided knife.
South Australian Police confirmed that no personal data had been breached during the incident.
Since the outbreak of the pandemic, many pubs and restaurants moved quickly to install QR code systems.
They can hold a massive amount of data compared to standard barcodes - up to 2,500 numeric characters, compared to a barcode's 43.
That means useful information, including names, locations and website addresses, can all be reliably and cheaply held in one small box.