Earlier this year, Johnson resolved to grant planning permission for an office-led redevelopment at Blossom Street, London. The former mayor's decision overturned Tower Hamlets Council's decision to refuse planning permission.
Spitalfields Historic Trust Ltd secured permission to make a judicial review application.
The Trust claimed that the former mayor had acted unlawfully. It argued that the statutory criteria required in order for the mayor to make a direction had not been satisfied and that Johnson had failed to consider a material consideration, namely the Trust's letter and that the "officer's report had not been an objective assessment".
Mr Justice Gilbart dismissed the Trust's challenge on all grounds and ruled that the former mayor's decision was lawful.
The judge concluded that the points addressed in the Trust's letter would not have "led to a different decision" and that the officer's report was "a very full and comprehensive one, which deals with all the objections to the development very fairly".
He also held that the statutory criteria had been fulfilled and that "the argument that the development would not have a significant impact on the implementation of the spatial development strategy is one without any merit".
Mr Justice Gilbart also stated that "as the question of the cross boundary effects, the site lies within the immediate vicinity of both the City of London and of Hackney. There can be no question that there will be some effects".
Planning expert Richard Ford of Pinsent Masons, the law firm behind Out-Law.com said: "Hopefully this saga will soon be over. The interesting question is what would new mayor Sadiq Khan have done by way of decision on this? It may not have been the same outcome. I expect to see many more mayoral call-ins post the Housing and Planning Act changes to allow the mayor to call-in more applications by reference to the London Plan. "
"GLA officer reports will need to be very robustly drafted to avoid an increase in challenges against GLA decisions. It is clear from this decision that, although the GLA decision was considered lawful, great care is needed to ensure all the points at issue are covered fully," said Ford.