The company had demanded compensation alleging that slow decision making and inflexibility of the LU resulted in cost overruns for upgrading the Jubilee and Northern lines.
The claim was dismissed by an independent adjudicator who found it "labyrinthine, artificial and unconvincing." Tube Lines will now probably have to meet the entire cost of the overruns itself.
The upgraded signalling system on Jubilee Line was supposed to be operational by the end of last year, but will likely require many more months for completion.
The introduction of the system on the Northern Line may also be delayed as a result.
The cost overrun on the Jubilee line will reportedly cost the company about £50m.
Tube Lines said it was disappointed with the ruling and will study the adjudication before deciding whether to file an appeal.
LU welcomed the ruling, saying it makes it clear that Tube Lines is responsible for the costs it has incurred as a result of delays to the upgrade of the Jubilee and Northern lines.
Tube Lines, co-owned by Ferrovial of Spain and Bechtel of the US, holds a long-term contract for maintaining and improving the busy Jubilee, Northern and Piccadilly lines.