The effort to impose the changes has become something of a proxy fight between the administration and the two largest municipal worker unions - DC 47 and its blue-collar counterpart, District Council 33.
The unions, which have 12,400 members, have gone three years without a contract.
Cathy Scott, president of DC 47, said Nutter was violating 40 years of tradition by seeking to impose changes on Local 2186 before reaching an agreement with DC 47.
"Unfortunately, we have a mayor who doesn't know how to negotiate. He thinks he can dictate everything," Scott said outside the commission hearing. "We're dealing with someone who is petulant. When he doesn't get what he wants he just walks away."
Nutter announced last month that he would give raises to about 5,500 nonunion and supervisory employees, while imposing benefit changes he had been unable to secure at the bargaining table.
He needs the commission's permission to make work rule changes affecting Local 2186 employees, and City Council's blessing to change the pension system.
The overall package would raise city costs just $17 million over five years, representing the kind of affordable deal - offsetting salary increases with benefit savings - that Nutter has sought from the municipal unions.
The unions countered that the raises would not cover the cost of the pension and health-care changes, netting a pay cut for struggling city workers.
The changes approved Wednesday still face a Nov. 16 review before the Administrative Board, which consists of the mayor and the city's managing director and finance director. The changes then would sit for 30 days, allowing anyone to object.
Scott said the union would object - sending the matter back to the Civil Service Commission - and was considering filing an unfair labor practices charge.
The commission meeting lasted several hours, as Local 2186 President Michael J. Walsh rose to object to each change, asking unsuccessfully that they be pulled from the agenda.
"There are 41 different changes. Everyone is going to read them and see different things," he said. "That's why I think we need to slow down and have a public hearing."
Contact Troy Graham at 215-854-2730 or tgraham@phillynews.com, or follow on Twitter @troyjgraham.
