Mrs Justice Laing in the Planning Court in London dismissed all three legal challenges by former ICE president Mark Whitby to the Ordsail Chord rail project.
He was also refused permission to appeal.
The Skanska and Bam Nuttall joint venture which is developing the scheme can now continue with the project.
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A spokesman for Network Rail said: "We welcome this decision as the Ordsall Chord forms a key part of our Railway Upgrade Plan for the north of England.
"More than £1bn is being invested to provide passengers with better services and we plan to start work on the Ordsall Chord as soon as possible."
The 340m long viaduct will join the Bolton line with the Chat Moss line, crossing the Irwell on a new bridge.
The Ordsall Chord will link Manchester's three main railway stations - Piccadilly, Victoria and Oxford Road – improving capacity and enabling faster, more frequent services between towns and cities across the north, along with the creation of a new direct routes to the city's airport.
(LM/MH)
