Dozens of customers earlier took to social media to report the issue.
The outage has also shut down entire stores.
A woman named Rose, from Hoppers Crossing in Melbourne, told 3AW customers were offered lollies as they were asked to leave.
News Corp Australia counted at least ten abandoned trolleys and baskets in the store.
In a statement, Woolworths said the outage was related to an IT systems update before registers came back online by about 4.30pm.
Woolworths has apologised after a technical glitch knocked out thousands of registers across the nation for close to an hour, forcing some stores to shut.
"The registers are now back online in all our stores", the company said. "We apologise for the inconvenience this caused our customers".
Stores temporarily closed in response to the outage.
The issue began affecting all registers across the country shortly after 4pm, leaving consumers with trolleys full of shopping but no way to pay.
Registers have shut down with stores unable to make sales.
The supermarket giant has taken to Twitter to confirm the IT issue has since been resolved.
The ABC reached out to Woolworths for comment.