Kiyoshi Kimura, who owns the Sushizanmai chain, paid 333.6 million yen ($3.1 million) for the 278-kg fish caught off the coast of northern Japan's Aomori prefecture, or double what he had paid 6 years ago.
"The price was higher than originally thought, but I hope our customers will eat this excellent tuna", Kimura said after the auction.
Saturday's event was the first New Year auction of the Toyosu market, after the famed Tsukiji fish market shut last year to provide temporary parking for the Tokyo 2020 Summer Olympics.
He spent more than twice the previous record of $1.4m, which he paid in 2013.
President of sushi restaurant chain Sushi-Zanmai, Kiyoshi Kimura (R), displays a 278kg bluefin tuna at his main restaurant in Tokyo on 5 January 2019.
Last year's auction was the last at Tsukiji before the market shifted to a new facility on a former gas plant site on Tokyo Bay.
The final New Year's auction at Tsukiji in 2018 saw a tuna fetch 36.45 million yen.
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Hundreds of sushi lovers queued for a taste.
The Japanese are known to be the biggest consumers of the torpedo-shaped bluefin tuna, and the growing consumption has led to overfishing of the species.
Experts warn it faces possible extinction, with stocks of Pacific bluefin depleted by 96% from their pre-industrial levels.
Opened in 1935, Tsukiji was best known for its pre-dawn daily auctions of tuna, caught from all corners of the world, for use by everyone from top Michelin-star sushi chefs to ordinary grocery stores.
The Tokyo metropolitan government decided in 2001 to relocate the aging Tsukiji market to Toyosu, but the initial plan to open the new market in 2016 was pushed back following the discovery of pollutants and subsequent decontamination work.
"I sincerely hope this market will be loved by many people", said Tokyo governor Yuriko Koike, who attended the sale, wearing the white rubber boots favoured by auctioneers.
However issues including concerns about outdated fire regulations and hygiene controls prompted the market to be moved to a larger and more modern site.