Thomas, 38, led the Bruins to the Stanley Cup championship in 2011 but has not played this season.
The Bruins acquired a conditional second-round pick in 2014 or '15 in the deal.
The move is believed to be purely a cap-related transaction. While the Bruins receive cap space from clearing the last year of Thomas' four-year, $20 million contract from the books, the Islanders add some insurance to reach the cap floor.
"He was a great, significant part of our Stanley Cup-winning team. He had a very good career here, and I can't say enough about his contributions to the team," Bruins general manager Peter Chiarelli said. "The journey he took us on in the Stanley Cup was amazing, and I was happy to be along for the ride."
Added Islanders general manager Garth Snow: "We traded for an asset, and it gives us some flexibility moving forward."
Thomas announced via his personal Facebook account in June that he was taking a year off to spend more time with his family. He held true to his word once the lockout ended and was subsequently suspended by the Bruins.
A source told ESPN.com's Pierre LeBrun that Thomas still doesn't want to play this season. In addition, the Bruins did not need his permission to trade his rights; his no-trade clause disappeared after last season.
"Thomas' situation is status quo," Thomas' agent, Bill Zito, told ESPN The Magazine's Craig Custance. "As far as I know, none of this had anything to do with Tim. In fact, it was news to us when we learned of it."
Assuming he does not play, Thomas will remain suspended (as he was by the Bruins), and the Islanders will not have to pay him any actual salary. Because he has a 35-plus contract, his salary-cap charge counts regardless of whether he plays.
Snow also said he had not considered whether he will "toll" Thomas' contract if he does not report.
"I haven't had any conversations internally regarding that, so, to answer your question, we haven't even considered that," Snow said.
When asked whether he actually wanted Thomas to play, Snow sidestepped the question by calling him a "world-class goaltender" with a "great résumé."
Thomas, a two-time Vezina Trophy winner as the NHL's top goalie, has played in 378 regular-season games -- all with the Bruins. He is 196-121-45 with a 2.48 goals-against average and 31 shutouts, and ranks fourth on Boston's career wins list and third in shutouts.
He also has a 29-21 mark in the postseason with a 2.07 GAA and six shutouts. Thomas won the Vezina and Conn Smythe Trophy as playoff MVP when the Bruins won the Stanley Cup in 2011.
"I've had discussions on and off with the Islanders, regarding this for a while," Chiarelli said. "I don't really want to get into detail. I think I've made it known publically that this is something we would like to try and do at some point, and then build some backside protection into it with the draft pick. I can't speak for Garth, but I know they see him as an asset."
NHL deputy commissioner Bill Daly told ESPN.com the league doesn't negatively view the trade, which appears to be a salary-cap maneuver.
"As long as a player has an active contract that he has the right to return to, absent unusual circumstances, our view is that he remains a 'hockey asset' that a club has a right to trade or acquire," Daly said.
Information from ESPN.com's Pierre LeBrun, ESPN The Magazine's Craig Custance, ESPNBoston.com's Joe McDonald and The Associated Press was used in this report.