Orient's lawyers argued in the High Court in London that the London Legacy Development Corporation (LLDC) tenancy agreement with West Ham was "entirely flawed".
The League One club called for a judicial review because they were "never properly considered as a co-tenant with Premier League side West Ham".
However, the LLDC argued that some of Orient's points were "wholly illogical", their case was "devoid of merit" and their Decision Letter clearly explained the process.
Following the hearing, which lasted over two hours, Mr Justice Lewis refused Orient's application for a judicial review.
Orient previously failed in a written application in April to get a judicial review.
West Ham issued a statement on their website welcoming the news.
It read: "West Ham United welcome the decision to not grant permission for a judicial review into the LLDC's process that awarded the club the opportunity to make the Olympic Stadium its home in 2016.
"Although the application for a judicial review would not have had any impact on West Ham United's move to the Queen Elizabeth Olympic Park, the Club have always believed the process was robust, fair and transparent.
"The club and other key stakeholders in the Queen Elizabeth Olympic Park can now focus fully on progressing their ground-breaking plans to create a stunning venue of which the whole country can be proud, alongside a long-lasting and tangible Olympic legacy with a real community club at its core.
"West Ham United will continue its consultation with supporters to ensure the Hammers' new home is the pride of east London and the envy of the rest of the footballing world."