"Nevertheless, the SRC did not have the authority" to suspend part of a 2008 law that prohibits districts from limiting enrollment at a charter unless the school agrees, the judge ruled.
Glazer also said the SRC could not prohibit charters from seeking payment from the state Department of Education for students enrolled beyond the limit set by the district. Payments from the Department of Education to the charters are deducted from money the state sends to each district.
The suits were filed separately in 2011 after the district, despite the 2008 law, continued to set limits in charter enrollment. They were later combined.
Philadelphia school officials recently said the cash-starved district might spend nearly $700 million on charter payments by the end of the school year - $25 million more than budgeted. One of the main reasons is that charters have enrolled 1,600 more students than permitted in their agreements.
Kevin McKenna, an attorney who represents three of the charters that filed the suit, hailed the ruling.
"We think this is a significant decision for all charter schools in the city," he said, "and especially those who were courageous enough to file suit."
He said the ruling meant that the schools that challenged the SRC could not have their enrollments capped and could not be barred from asking the state to pay for the additional students if the district refused.
"We would hope the district would abide by the decision and move forward," McKenna said.
The ruling directly affects Richard Allen Preparatory School, Southwest Philadelphia; Delaware Valley Charter, Logan; Walter D. Palmer Leadership Learning Partners, Northern Liberties and Frankford; Wakisha Charter, North Philadelphia; and Folk Arts Cultural Treasures Charter, near Chinatown.
"We are in the process of reviewing the opinion and considering our alternatives for responding to this decision," Fernando Gallard, a district spokesman, said in a brief statement Wednesday.
"The decision does not in any way preclude the district from moving forward with recommendations and actions that are in the best interests of students and families, including those that will be made at the School Reform Commission meeting" Thursday, he said.
The five-member commission is scheduled to vote Thursday on a new charter policy that is based on heightened powers stemming from the recent suspensions of the law covering charters.
The SRC is also set to vote on revoking Palmer Leadership's charter.
Superintendent William R. Hite Jr. said Tuesday that he would urge the commission to halt payments to the school July 1 and to begin revocation proceedings because of allegations of poor academic performance, serious financial woes, and billing for students not enrolled.
The judge's opinion comes as debate intensifies over the SRC's powers and as three other suits about those powers are pending in the state Supreme Court.
Two of the cases deal with charters. In the third, the SRC has asked the state's top court to declare that the commission has authority to disregard seniority in making teacher assignments and impose other work-rule changes in the fall.
The 11,000-member Philadelphia Federation of Teachers has asked the court to toss out the SRC's petition.