Javid had refused planning permission for the site off Hamble Lane in November last year, despite the council being unable to demonstrate a five-year housing land supply.
He acknowledged that the project would bring social benefits in providing much needed affordable homes in the area. But he said it would cause "environmental and social damage" by filling in the gap between existing settlements.
The development would be "physical intrusion" into the countryside and the benefits of the scheme were outweighed by "adverse impacts", Javid argued.
Developer Hallam Land Management challenged Javid's ruling, but today had their complaints rejected by Mr Justice Supperstone.
Just a few days after rejecting Hallam’s proposals, Javid granted planning permission for 680 homes, a care centre and a primary school on land to the north west of Boorley Green, also within Eastleigh Borough Council's area.
But the judge rejected arguments that the two decisions were "irreconcilable" or that Javid's decision was "irrational".
Eastleigh Borough Council accepted that there was a five-year housing land supply shortfall, estimating that it had enough housing land to last 4.86 years.
Hallam, meanwhile, argued that the right figure was "not more than 4.25 years", but Javid described the shortfall as "limited".
The judge rejected Hallam Land's arguments that Javid was obliged to give a precise figure on the housing land shortfall.
The judge ruled that the Boorley Green scheme was granted consent on the basis of "different evidence" and there was no fatal inconsistency between the two decisions.
Hallam Land Management Limited v Secretary of State for Communities and Local Government & Anr. Case Number: CO/6439/2016