ITV's 15.5m shares in Thomson originate from Carlton's sale of manufacturer and distributor Technicolor to Thomson in 2001.
The estimated £162m proceeds from the sale will be used to reduce ITV's debt burden.
The merger of Carton and Granada to form a combined ITV earlier this year led to speculation that its non-core assets would eventually be sold.
The process began last month when ITV sold its publishing arm, Carlton Books, to a management buyout team for £3m.
Other businesses expected to be sold include: post-production unit The Moving Picture Company; cinema ad business Carton Screen Advertising; and a stake in SMG, which owns the Grampian and Scottish Television ITV franchises.
ITV will also sell its 10% stake in Liverpool Football Club and its 5% stake in Arsenal. The holdings are valued at £18m, a fraction of what Granada originally paid.
The next biggest prize after Thompson is Carlton Screen Advertising, which is worth as much as £66m.
Charles Allen, chief executive of ITV, said: "We're delighted to have sold our non-core asset sooner than expected at a five-month high and reduce our borrowings by £172m."
He added: "This disposal, together with the recent sale of Carlton Books and the initial bids we've received for The Moving Picture Company, means that we are well advanced in disposing of our non-core assets."
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