The system is a joint initiative between the department and the South African Banking Risk Information Centre (SABRIC).
In terms of the initiative, the department will allow banks access to the Home Affairs National Identification System to verify the identity of prospective and current clients using their fingerprints.
Five banks - ABSA, African Bank, FNB, Nedbank and Standard Bank - are currently participating in the initiative, with the system at different phases of implementation with each bank.
Dlamini Zuma thanked SABRIC for the support and confidence it had shown in her department by partnering with it.
"We equally, as government, through this partnership, express our confidence in the South African banking system which has weathered the storms of various stages of our economic development including, the recent global recession," she said.
The launch also laid the foundation for a more strategic partnership between the department and the banking sector, the minister noted.
"In launching the Online Fingerprint Verification System, Home Affairs and SABRIC indeed contribute to a positive climate in which our citizenry are and feel safe in the knowledge that their savings, investments, deposits and hard-won earnings are indeed secure in the hands of the various banking institutions," she added.
SABRIC described the initiative as an important measure in helping banks prevent identity theft related crimes that banks and its customers become victims of.
SABRIC CEO Kalyani Pillay said: "The banks are very grateful to the Department of Home Affairs for allowing them this unique opportunity to maximise the benefits of technological innovations in the interests of their clients.
"Banks clients will benefit immensely from this initiative as it offers the banks a second layer of confirmation that the persons presenting identity documents are indeed who they purport to be."