Giles, 37, was claimed on waivers by the Red Sox, and Boston and San Diego had 48 hours to make a deal. But the Red Sox are one of eight teams listed in the limited no-trade provision in his contract, and Giles had the right to veto the deal.
It is not unusual for older players such as Giles to turn down such deals. Among the issues that came up was location -- Giles, who grew up in San Diego, did not want to leave family behind -- and there was the concern about playing time with the Red Sox.
He wouldn't say who killed the deal -- several reports said he refused to give his consent.
"It's kind of between myself and my agent and Boston and the Padres," Giles said, according to The Associated Press. "I don't think really anything needs to be said other than I made a commitment to play for this team for three or four years, and at the end that's where I still stand."
The Red Sox and Padres had been hopeful that a deal could be worked out -- Boston wanted Giles because of the offensive depth he would provide, and San Diego could have saved at least $6 million if the All-Star right fielder had accepted the move.
The deadline for a deal to be worked out was 1:30 p.m. ET Friday.
Giles is hitting .296 with a .391 on-base percentage, 61 walks and 44 strikeouts this season.
Giles' agent, Joe Bick, would not acknowledge or speak to the involvement of the Red Sox in the waiver claim, and he wouldn't discuss the question of whether there were any talks about a contract extension.
But Bick did say that "in the final analysis, Brian said, 'I made a commitment to the Padres three years ago that I would like to fulfill. And it's my hope that at the end of the current season, that they would elect to pick up my option for next year, and I can finish my career with the Padres.'"
San Diego holds a $9 million option on Giles for 2009, with a $3 million buyout. "We thoroughly discussed and analyzed and projected the next two or three years of his career," Bick said, "and took in every consideration, and he made the decision that he made. He has never made a decision based on what was best for him moneywise. He took a deal from the Padres that was $6 million to $9 million less than what he could have gotten elsewhere. The money factor had very little to do with his decision."
Giles, who grew up in the San Diego area, wants to finish his career with the Padres.
"I don't know how many years I have left," he told The Associated Press. "I've had a good time here in San Diego. Like I've preached before, the same games we've been the last couple of years that we've won we haven't won any of those this year. Given our division and how young it is, it's going to be inconsistent for the next two or three years, so I feel there's an opportunity here. Obviously, there are pieces missing and we need to address those pieces.
"I've had a couple of dings this year, but I've been able to take some days off. I know I have a few years left; hopefully it is with San Diego."
Buster Olney is a senior writer for ESPN The Magazine. Information from The Associated Press was used in this report.