Nutter said similar wage increases awarded to police officers last year - which he did not appeal - were not offset in the fire contract by sufficient health-care savings or the ability to require furloughs.
City Finance Director Rob Dubow said the contract would cost the city an additional $146 million over the next five years, including nearly $80 million in health-care costs.
Nutter said the police award afforded the city ways to offset costs but the firefighter contract did not, "short of simply cutting services."
"This award is bad in the short term and worse in the long term," Nutter said. He has 30 days to appeal to Common Pleas Court.
Nutter said he would appeal the furlough issue - he won the right to require unpaid leave of police officers for up to two weeks a year - and almost all wage and benefit aspects.
The administration also will appeal provisions that prevent the city from eliminating certain jobs regarded by the union as vital, and a provision that would change the testing process for battalion chiefs and deputy chiefs.
Nutter will not appeal the 401(k)-type pension plan that will be offered to new employees, which affords the city some long-term savings but little up front.
New firefighters who opt to stick with the traditional pension plan will have to contribute 6 percent of their salaries, instead of 5 percent for current department employees.
Unlike police, who for the first time will be exempted from the city's residency requirement, firefighters will still have to live in the city.
The more than 2,100 firefighters have been operating under the terms of a contract that expired more than 15 months ago.