Maynards' Fine Art and Antiques says one of the paintings — a landscape believed to be by Tom Thompson — sold Wednesday night for $126,500, which is half the estimated price.
The other painting, a watercolour by Frederick Varley, whose later works were part of the Group of Seven painters, fetched $7,475, with both sale prices including a buyer's premium.
The artworks were brought to Maynards in January by a man who said he paid $100 for them at the East Vancouver yard sale.
The untitled landscape oil painting, in pale blues, purples and peachy colours and measuring 28 centimetres by 21 centimetres, was expected to sell for $150,000 to $250,000.
The auction house says the artworks were authenticated by some experts, while others remain skeptical about the supposed Thomson painting.
"We at Maynards are pleased on behalf of both the consigner and buyer of these pieces of true Canadian fine art," said Kate Bellringer, Maynards' director of contemporary art.
"It was a smart purchase, a good investment and a great ending to an incredible story."