Kelly, 59, was handed a bill made up of almost £900,000 in income tax and more than £300,000 in national insurance contributions in 2016.
From 2012, she was contracted to present Daybreak and her Lorraine show through the company she runs with her husband.
But HMRC argued she was effectively an employee of ITV.
Judge Jennifer Dean sided with Kelly after she launched an appeal claiming she should be treated as a “self-employed star”.
In a ruling by the first-tier tax tribunal, the judge concluded the relationship between Kelly and ITV “was a contract for services and not that of employer and employee”.
She also said Kelly can be described as a “theatrical artist”, meaning payments to an agent were allowed as a tax-deductible expense.
The judge ruled: “We did not accept that Ms Kelly simply appeared as herself - we were satisfied that Ms Kelly presents a persona of herself, she presents herself as a brand and that is the brand ITV sought when engaging her.
“All parts of the show are a performance, the act being to perform the role of a friendly, chatty and fun personality.
“Quite simply put, the programmes are entertaining, Ms Kelly is entertaining and the ‘DNA’ referred to is the personality, performance, the ‘Lorraine Kelly’ brand that is brought to the programmes.”
She added: “We should make clear we do not doubt that Ms Kelly is an entertaining lady but the point is that for the time Ms Kelly is contracted to perform live on air she is public ‘Lorraine Kelly’.
“She may not like the guest she interviews, she may not like the food she eats, she may not like the film she viewed but that is where the performance lies.”
The tribunal found Kelly was free to carry out other work and activities and did not enjoy employee benefits such as sick pay and holiday pay.
A HMRC spokesman said it was “disappointed” with the ruling, adding: “We will carefully consider the outcome of the tribunal before deciding whether to appeal.”