Can I pay my employees' super?

Yes, superannuation contributions can be made through pay.com.au, in the same way you would make other payments. 

This is how you can make superannuation payments through pay.com.au depending on the way the individual's superannuation is setup.

When superannuation is paid to the individual, use the payroll flow. If the employee has a SMSF, this can be completed via the payroll flow, with the payee details as that of the employee. 

When superannuation is paid directly to a superannuation fund, use the supplier flow. You should complete this through the supplier flow and input the payee details (ABN, BPAY biller code and CRN or BSB and account number) of the super fund or clearing house.