The bank apologised after some customer payments were unexpectedly repeated on Saturday morning, allegedly leaving some accounts overdrawn.
The number of people impacted and the reason behind the issue have not been made public.
The bank said it had completed the process to reverse duplicate transactions and addressed other issues with its app by 5.30pm AEDT.
"We're sorry for the inconvenience," the company said.
"Thanks for being patient with us.
"Please be assured any fees charged will be refunded.Â
"Customers do not need to contact us to request this."
An earlier statement about the glitch the bank posted to social media prompted complaints from customers.
Some shared their concern that their accounts were overdrawn.
The latest incident came after the bank on Thursday apologised and agreed to pay $7.5 million after sending 170 million emails that breached Australian anti-spam laws.
The marketing messages sent to CBA customers between November 2022 and April 2024 breached the Spam Act 2003 because they did not include a way to unsubscribe, the Australian Communications and Media Authority said.
A total of 34 million messages were sent to people who had either not consented or who had withdrawn their consent to receive such messages, the authority said.
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