Agencies report the ruling came at the start of a hearing into a lawsuit filed by Puma, the maker of the uniforms, against soccer's governing body, which banned them.
"There is nothing there that says shorts and shirts must not be linked together," Judge Ingrid Kefer said.
She said FIFA applied its rules arbitrarily and broke cartel regulations. Puma is seeking $2.6 million in damages from FIFA and wants a ruling that it can market the uniform.
The judge gave FIFA four weeks to respond and give a written statement. A final ruling is expected June 1.
FIFA rules state players are to wear "a jersey or shirt" and "shorts." FIFA says that means separate garments. FIFA fined Cameroon last April for wearing the one-piece uniforms during the African Cup. It also docked the country six points in its qualifying campaign for the 2006 World Cup.
Cameroon and Puma had said they received approval to wear the uniforms from the African Soccer Confederation.
Puma contends FIFA's decision was influenced by rival Adidas, which works closely with FIFA.
