The Mets finished second with a bid between $39 million and $40 million, according to a baseball official who spoke on condition of anonymity because none of the losing bids were revealed. The Yankees bid between $32 million and $33 million, another baseball official said.
Matsuzaka was scheduled to fly to the United States on Wednesday and give a brief news conference at the airport.
Even before the Matsuzaka announcement, general managers had assumed Boston would be the highest bidder in the blind process.
"We'll congratulate the winner and move on," New York Yankees GM Brian Cashman said Tuesday afternoon.
The Chicago Cubs and Texas Rangers also were thought to be among the bidders.
"I'm very comfortable with the bid that we made," Mets general manager Omar Minaya said, sidestepping whether he would have topped Boston's offer now that he knew what it was.
Bidding closes Friday for Akinori Iwamura, a third baseman with the Central League's Yakult Swallows, but sources told ESPN's Peter Gammons that Tampa Bay Devil Rays have posted a winning bid of $4.5 million for the rights to negotiate with Iwamura. Iwamura, 27, batted .312 with 32 homers for Yakult in 2006.
Before the Matsuzaka announcement, agents roamed the hotel lobby, discussing their free-agent clients.
"Pitching, as usual, is at a premium," Boras said.
Information from The Associated Press was used in this report.