The issues were caused by an upgrade that was carried out on Thursday and did not go according to plan.
The CBA added that its staff had been working on the issue overnight and that it was trying to clear the backlog as soon as possible.
On Thursday, ATMs — apart from cardless cash and cardless deposits — EFTPOS merchant services, debit and credit cards were all working.
The bank said all branches would open as normal on Friday, adding that there would be a delay experienced by those who contacted call centres.
"We have brought in additional staff to serve customers to assist with any outstanding issues," the statement said. "We are very sorry for the inconvenience this is causing our customers.
Imagine being a company that literally steals money from their customers, makes billions of dollars and yet can't provide a basic service to not one single customer #commonwealthbank— Oz (@ausmojo) October 17, 2019
"We want to assure customers that their accounts are safe. The internal system issues related to an upgrade implemented on Thursday."