Nathaniel Hepburn MBE, director and chief executive of Charleston, said: “Bringing this painting back to Charleston is a moving and important moment.
“It reunites us with a work that Duncan Grant lived with every day and adds a rare example of collaboration to our collection.”
He also thanked the Arts Council England.
Flowers in a Jar, created during the period of Grant and Bergen’s love affair, stands as a record of Grant’s personal and artistic relationship with the Russian painter.
The painting’s return also comes as Charleston launches Studio 100, a campaign to raise £250,000 for essential repairs and sustainability upgrades.
Mr Hepburn said the campaign could “conserve the studio itself and safeguard its legacy for generations to come”.