The partnership, due to be unveiled by Microsoft chairman Bill Gates in a keynote speech at the RSA Conference in San Francisco, forms one of the next steps in Microsoft's drive to improve security.
A single log-in will give organisations the ability to record and keep an audit trail of every user that has accessed the systems, either from within the company or externally.
The technology will become increasingly important to help businesses comply with financial regulations, such as Sarbanes-Oxley and Basel 2.
"For highly regulated markets, access to corporate data and sensitive client information is becoming more restricted. The knowledge of who is accessing what becomes more important," said Tim Pickard, strategy marketing director at RSA.
Software developed by RSA with support from Microsoft will allow organisations to replace their standard Windows password log-in with an interface requiring a secure-token log-in.
It will allow organisations to provide secure access to laptop computers, even when they are not connected to the corporate network. This can protect businesses from losing confidential data if employees have their laptops stolen.
RSA said the technology would dramatically improve the security of corporate systems by verifying the identity of everyone accessing the internal network and eliminating the need for users to remember multiple passwords.
"When you have one or two applications, users can remember their passwords. As that number grows to nine to 15, it becomes unmanageable," said Pickard.
RSA said the technology could save firms more than £100 a year per employee, simply by eliminating the need to reset forgotten passwords.
RSA plans to conduct beta trials of the new technology with large businesses over the next few months.