On social media, shoppers around Australia said they had been told to leave their trolleys and leave the store on Monday afternoon.
Signs were put up at a number of Woolworths stores apologising for the problem.
By 4.30, however, Banducci announced "our systems ultimately (have) self-corrected themselves", and the supermarket came back online.
Registers shut down with stores unable to make sales shortly after 4pm, leaving consumers with trolleys full of shopping but no way to pay.
Woolworths is turning customers away from its stores, following reports the Australian supermarket chain is suffering a nationwide IT outage.
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A Woolworths spokeswoman said the registers were coming back online now.
Staff working at one of the affected stores, at Sydney's Town Hall, earlier confirmed the outage meant customers forced to leave without their purchases.
"We can confirm that an IT issue impacted registers in our supermarkets for a short period of time this afternoon", a spokesperson for the supermarket chain told Computerworld.
The ABC reached out to Woolworths for comment.