The review of super guarantee payments follows complaints from six part time CBA employees brought to the attention of the bank by the Finance Sector Union and reported by the ABC last week.
In a statement to the ABC, a CBA spokeswoman said: "we agree these hours worked should have superannuation applied and we want to do the right thing by our people".
"If we identify an employee who is owed superannuation, we will reimburse it."
The CBA will repay super to all part time workers since 2009 including those who have switched to full time positions or have since left the bank.
The bank is yet to put a number on the staff set to be repaid, though last week the FSU said it could exceed 7,000 staff.
The average payment is $180 per year on average according to the CBA although in some cases the figure could be as low as four dollars.
While the reimbursements are tiny compared to the value of Australia's biggest home lender, the FSU had threatened to take the complaints to Fair Work Australia which could further harm the CBA's battered reputation.
The CBA is currently in constant damage control amid fallout from scandals at its financial planning division and life insurance arm CommInsure.
However, the CBA maintains is was not breaking the law by only paying superannuation on ordinary hours rather than extra hours or overtime.
The statement says the bank's policy was based by a superannuation guarantee ruling issued by the Tax Office in 2009.
The superannuation backdown comes as Australia's Big Four bank chief executives prepare for their six month grilling by the House Economics Comittee in Canberra.
Commonwealth Bank chief executive Ian Narev is scheduled to face the committee on Tuesday.
Separately, a senate committee is investigating claims by Industry Super Australia and Cbus that around a third of Australian workers are being ripped off by rogue employers who are holding back some or all of their superannuation entitlements.