Chippendale, from Otley, was commissioned to furnish the newly-built seat of the Lascelles family in 1767 and it became the most significant project of his career.
Among the bespoke furniture he designed exclusively for Harewood House were two pier tables with looking glasses.
The family have opted to donate the historic treasures to the nation in lieu of inheritance tax.
They have been acquired by the London-based V&A, but will remain on display in the music room at Harewood on a loan basis.
The pieces have been described as representing the pinnacle of Chippendale's craftsmanship.
V&A director Tristram Hunt said:
"It is exceptionally rare to find Thomas Chippendale furniture as well-documented as that at Harewood House - the most lavish commission Chippendale ever received.
"Of superlative quality, the tables and glasses are welcome additions to the V&A's world-class collection of English furniture.
"We are delighted that they can remain in their original location to be seen and appreciated by visitors to Harewood House for years to come."
V&A conservators will now restore the surface finish of the objects closer to Chippendale's original intention.
The Harewood House Trust has been marking the 300th anniversary of Chippendale's commission with special exhibitions.
He provided the Lascelles family with tables, chairs, sofas, beds, commodes, mirrors, curtains, pelmets, wallpaper, carpets and even garden benches.
His most magnificent creation, the Diana and Minerva commode, is on display in the house.
In May, curators at Nostell Priory, near Wakefield, discovered hidden drawings behind a 12ft mirror made by Chippendale.
Its removal for restoration for the first time since the 19th century revealed that the renowned master craftsman had papered around the edges of the showpiece pier glass in the state apartment.
The mirror was originally installed for Sir Roland Winn, a client of Chippendale's whose family lived at the Palladian mansion until the National Trust took it on in the 1950s.
Chippendale appeared to have taken steps to avoid decorating the wall behind the mirror with expensive, hand-painted Chinese wallpaper where it would not be seen. Winn is believed to have haggled down the price of 18 sheets of the paper, which had been imported by the East India Company. The furniture maker's original markings were found on the back of the mirror, where they had been added as a guide for the glazier.