The property, at Beveridge about 60km north of Melbourne, includes a run-down weatherboard cottage that was built by Kelly's father and where the Kelly family lived from 1859 to 1864.
It sold for $640,000 - there is a newer four-bedroom home also on the property.
Ray White Real Estate senior saleman Rocco Di Battista said the buyers were a family from nearby Craigieburn who "fell in love with the home and its surroundings".
"They looked at the Kelly Cottage as a long-term thing ... as something of significance and something that you can't replace," Mr Di Battista told AAP on Saturday.
"They would love to see it refurbished or for someone to come along with the money to do it."
He said the auction attracted three bidders plus about 250 onlookers, a "sausage sizzle, clowns, a couple of Irish people playing Ned Kelly ballads and a guy who rocked up on a horse with a driza-bone and a Ned Kelly hat on".
Kelly Cottage was classified in 1984 by the National Trust Victorian branch (NTV), and added to the Victorian Heritage Register in 1992.
NTV is raising funds for the preservation of Kelly Cottage and, before the auction, had flagged a willingness to buy it if sufficient money could be raised.
"We weren't in a position to (bid) but that was never the main aim," NTV chief executive Martin Purslow told AAP.
"It's not necessary for the National Trust to own these buildings to look after them.
"Any funds we have raised are available to try and support anybody who has acquired it."
Donations can be made online at www.savenedkellyshouse.com.au.
