The proposed "Paddington Cube" is a 19-storey, 54-metre-tall office tower next to the grade I listed station and within the Bayswater conservation area.
Campaign group Save Britain's Heritage (SBH) claimed that the glass tower would permanently harm heritage assets in the conservation area.
Imperial College Healthcare NHS trust also objected that the development would increase journey times for ambulances going to St Mary's Hospital.
But now Mrs Justice Lang has rejected SBH’s judicial review challenge against Javid's decision not to call in the application.
The judge ruled that Javid had not been obliged to give reasons for letting Westminster City Council take the final planning decision on the scheme.
Great Western Developments Ltd was granted conditional planning consent for the project by the council in December last year.
In February, Javid issued an article 31 holding direction giving hiself more time to consider whether to call in the application, blocking the scheme from obtaining final approval in the meantime. In March, he decided not to call it in, meaning the council was able to grant permission.
In the High Court, SBH argued that it had a "legitimate expectation" that the secretary of state would give reasons for his decision.
Mrs Justice Lang accepted that it had been government policy to give reasons for call-in decisions between 2002 and 2014. However, she noted, this had now changed and such decisions were commonly made without reasons being given.
Javid, she ruled, was under no legal duty to explain why he was happy to leave the crucial decision to Westminster Council.
SBH's complaints that the decision not to call in the application was "made by civil servants", rather than Javid himself, "cannot succeed", she added.
In the judge's view, the objections to the Paddington Cube were "neither exceptional nor unusual" in such a high-profile case. And it was not a case in which SBH or other objectors "needed to see reasons" for Javid's decision, she ruled.
Save Britain's Heritage says it is considering its options, "including seeking leave to appeal, by which the battle can continue".
R (Save Britain's Heritage) v Secretary of State for Communities and Local Government. Case Number: CO/2023/2017