The councils argued that the failure of the commission's leaflet for residents to offer the option of retaining the status quo was perverse. But in an initial hearing last week, Mr Justice Latham ruled there was nothing irrational or perverse about the commission's draft recommendations and its consultations, and refused to allow a full judicial review.
The councils are considering whether to appeal.
The commission wants to establish three unitaries in the county. East Cambridgeshire wants to retain the status quo while the county wants two unitaries.
He also dismissed East Cambridgeshire's claim that it had a 'legitimate expectation' of the no-change option being offered for consultation.
After the ruling, Trevor Hardy, East Cambridgeshire chief executive, said the commission was backing retention of two tiers in Lincolnshire and most of Essex, and two tiers was the second option in Norfolk and Suffolk.
'I fail to understand why the people of Cambridgeshire are being denied the same choice that is being given to virtually every other area in the country,' he said.
Commission canvassing carried out before it published its draft recommendations in June showed 43% of the 971 Cambridgeshire residents who responded were in favour of the status quo.
Both councils said the court action had cost well under £10,000 each.
The Association of District Councils welcomed the decision.
'This is further, and I hope final, confirmation that disagreement with proposals put forward by the commission is not a valid reason to pursue judicial reviews,' said ADC chair Margaret Singh.
The court's decision was in line with previous rulings against Humberside, North Yorkshire, Somerset, Cleveland and Avon CCs, she said.