Am a bank employee. M i liable to pay back for money taken by fraud?

In this case you can defend yourself from paying the amount, since there is no lack of diligence and the Hon'ble Court acquitted the person because the person was not found guilty and hence, you cannot be made liable, as the person whom you paid has been found to be 'Not Guilty'. 

Since this proves that no offence has been committed, hence you are not liable to pay the amount.

In case the bank insists on you paying the amount, you must reply by requesting the bank to file an appeal in the higher court against the decision of the lower court citing non admittance and acceptance of valid case evidence (CCTV footage) by the lower court as the ground for appeal.