The week-long auction had over 1,300 bids and finished with a final offer of ¥6,011,000, according to Yahoo! Japan, who organised the event.
The singer used the cup and saucer while appearing at a Tokyo press conference three months after the tsunami in the country in March 2011.
Lady GaGa said at the time that she would auction the cup, before planting a lipstick kiss, signing it and writing the message "We pray for Japan".
The auction will raise money to help young Japanese artists who want to study in the US.
The teacup was the second most expensive item from the auction lot, with a piano owned by a Japanese rock star taking in the biggest bid.
Lady GaGa recently said that cocaine used to be her "friend" when she was younger.