Comyn was paid A$2.35m in 2017 and was among those who lost their short-term bonuses.
Comyn has led CBA's retail banking unit since 2012 and said the lender's size meant it had to be held to the highest standards.
"By virtue of the position CBA holds in the community we need to equally demonstrate the highest levels of integrity and operational standards to earn stronger levels of trust within the community and regulators," Comyn said after the announcement today.
"The last six months in particular have been very challenging and I am committed to working with the board, the executive team and our wonderful people to rebuild trust in the Commonwealth Bank."
Chairman Catherine Livingstone said Comyn, was best placed to maintain the bank's momentum and strong financial performance.
"In selecting the new CEO, the board considered, very carefully, which candidate would be best suited to manage the unique combination of the bank's commercial and operational priorities," Livingstone said.
"Of immediate concern, the bank currently faces a range of reputational, regulatory and legal issues that have overshadowed what has otherwise been very strong progress and performance."
Ms Livingstone would not discuss AUSTRAC's Federal Court case in detail but said Comyn was not solely responsible for any failings in the retail unit
"We regard this as an organisation-wide matter for which we all take collective responsibility," Livingstone said.
Narev announced in August he would leave the bank at the end of the 2018 financial year.