The virtually unknown Nicaraguan coffees, San Isidro and El Regreso, fetched $11.75 a pound - more than 20 times the current market price.
British coffee buyers Mercanta Coffee Hunters won the auction - held over the internet - for 16, 152-pound bags of the coffee on behalf of three retailers in the UK, Spain and France.
"The farmers were stunned after they were only offered only 20 cents per pound on the local market for this crop," Steve Hurst of Mercanta told BBC News Online.
International coffee prices are at their lowest level ever, selling at about 50 cents on the commodity markets.
Strong brew
It was the first year Nicaragua was admitted to the auctions, which also takes in Brazilian and Guatemalan producers.
"We are very pleased because the auction has surpassed all our expectations," said Roberto Bendana of Nicaragua's Specialty Coffee Association.
"In spite of the price crisis, this success should inject some enthusiasm back into the coffee industry here."
Peru, Colombia, Mexico, El Salvador and Costa Rica have applied to join the auctions, but first have to meet high production standards.
"What we want to show producers is that if you offer quality you get high prices," said Mr Hurst.
"Last week's Guatemalan auctions raised about $500m, which goes straight back to the farmers."
Coffee cupping
The previous record was held by Guatemala's Las Nubes coffee which went for $11 a pound.
The other 22 lots of Nicaraguan coffee sold for between $1.20 and $4 a pound, attracting buyers such as Japan's Unicafe and Batdorf & Bronson of the US.
The 23 coffees at auction were chosen earlier this year by a "cupping" contest, the equivalent of wine tasting.
The cuppings and auctions aim to differentiate high quality coffees from generic types selling on international commodity markets at rock-bottom prices.