Oakbay Investments, the controversial family’s main holding company, said it wasn’t aware that Baroda would close its accounts.
The bank’s South African unit, Absa, says the Competition Commission is not seeking any administrative penalty against it.
Local and international banks allegedly created fictitious bids and offers and co-ordinated trading times to distort demand and supply for profit.
The bank asked the High Court to prevent the president from intervening in its decision to close accounts of companies linked to the Gupta family.
South Africa remains at significant risk of having its debt downgraded to non-investment status, says the Reserve Bank.