Because the repayment was in the same year as the payment, you only need to repay the 'net' amount you received. The employer must file an amended 941 to recoup the withheld taxes.
If the repayment was in a different year than the payment, then you would follow Tom's directions in the other answer. You would need to repay the full amount, and then make an adjustment on your tax return for the year of the repayment.
This first link refers to the same situation when there is an "error", but as the second link shows, the same procedure applies:
https://www.irs.gov/publications/p15#en_US_2017_publink1000202537
https://tax.thomsonreuters.com/blog/cs-professional-suite/cs-payroll-solutions/overpayments-and-repa...
