The judge gave the Health Secretary permission to appeal against his decision.
A Department of Health spokesman said:
"This judgment applies to one aspect of a package of changes which we believe are in the best long-term interests of patients and the public across south east London.
"As it stands, the South London Healthcare NHS Trust has been running at a loss of about £1 million a week - money that has to be diverted from frontline patient care.
So of course we are disappointed by this decision. We need to consider the judgment carefully, and have obtained permission to appeal.
"We expect to continue other elements of that package of changes, including the dissolution of the South London Healthcare NHS Trust, planned for October 1 - although there are a number of steps to go before that can take place."