The legislation passed by city council last month would have required city businesses to provide paid sick days for employees.
The bill passed city council one vote shy of the total needed to override Nutter's veto.
A spokesperson for the mayor sent a message via Twitter that the burden on businesses would have cost jobs and made Philadelphia less competitive.
Nutter overturned a similar bill in 2011.
Several big corporations and the Pennsylvania Restaurant Association were also against the bill.