The move by one of Australia's best-known share managers could encourage other socially minded stock pickers to divest from Australia's "Big Four" banks on ethical grounds.
CBA has suffered a string of scandals over the past year that have included rate-rigging charges, breaches of anti-money laundering laws, and fees charged to dead clients.
Perpetual's divestment, disclosed in an investor update, places further pressure on Australia's banking sector to clean up its act as a powerful inquiry airs allegations of bribery, fee-gouging and board-level deception across the industry.
Perpetual's decision applies to its ethical Australian share product, which listed CBA as one of its largest holdings as recently as April. The fund manager has, however, retained its large CBA holding in its mainstream equities product.
A Perpetual spokeswoman said in a statement its ethical fund filters were tightened at the start of June.
"This included widening the definition of its governance (socially responsible investment) filter to capture more instances of corporate misconduct," the spokeswoman said.
An additional 25 companies were caught by the screens, Perpetual said in a statement to Reuters, without disclosing the names of the affected stocks.
CBA said in a statement it had nothing further to add to Perpetual's disclosures.
The "sustainable, responsible and impact" (SRI) investment sector housed $23 trillion around the globe at the end of 2016, according to the most recent biennial survey by the Global Sustainable Investment Review.
While Europe is the dominant region for such funds, SRI investments have increased rapidly in fossil-fuel-rich Australia from $148 billion to $516 billion between 2014 and 2016.
Revelations of poor practices have been flowing from the country's most powerful type of inquiry, called a Royal Commission, since the start of the year, testing the ethical screens of Australia's SRI funds which tend to focus on issues like a stock's exposure to uranium, alcohol, tobacco and gambling.
Investment consultant Mercer's global business leader of responsible investment, Helga Birgden, said governance issues were now being closely assessed by mainstream funds.
"Not because they label themselves as ethical or socially responsible, but because these are genuine and material investment risks," Birgden said.
CBA is one of Australia's biggest listed companies, with a market cap in excess of A$120 billion ($86.5 billion), making any decision to remove it from a share portfolio significant.
The quasi-judicial inquiry has also exposed bad business practices at National Australia Bank, Westpac Banking Corp and Australia and New Zealand Banking Group, along with fund managers AMP and IOOF Holdings.
The revelations have already cost AMP - itself a large fund manager that offers SRI products - several high-level resignations and about A$4 billion in market value.
Australian Ethical Investments said in May it was divesting its holdings in AMP.
(Reporting by Jonathan Barrett in SYDNEY; additional reporting by Paulina Duran; Editing by Stephen Coates)
By Jonathan Barrett