Dozens of customers earlier took to social media to report the issue.
Signs have been put up at a number of Woolworths branches apologising for the problem, which has been described as a "system fault".
Stores temporarily closed in response to the outage.
A woman named Rose, from Hoppers Crossing in Melbourne, told 3AW customers were offered lollies as they were asked to leave.
Registers have reportedly shut down at all Woolworths stores across Australia due to a technical outage.
"We can confirm that an IT issue impacted registers in some of our supermarkets for a short period of time this afternoon", the spokesperson said. At Haymarket in Sydney, customers were told to return in "an hour", according to one tweet for ABC journalist Michael Janda.
The grocer is yet to confirm the cause of the outage.
By 4.30, however, Banducci announced "our systems ultimately (have) self-corrected themselves", and the supermarket came back online.
Registers have shut down with stores unable to make sales.