Keller signed a one-year contract worth $4.25 million, according to a source.
"I'm with the team I want to be with," Keller told the South Florida media. "Everything is perfect right now."
The AFC East rivals appear to be headed in opposite directions. The Jets have lost five free agents while the Dolphins have waged a spending spree this week, signing wide receiver Mike Wallace and linebackers Dannell Ellerbe and Philip Wheeler.
Keller's departure comes two days after running back Shonn Greene bolted the Jets for the Tennessee Titans. Greene and Keller were key players on the 2009 and 2010 teams that reached the AFC Championship Game.
The Jets finished 28th in scoring offense last season, and it's not looking any better. Coordinator Marty Mornhinweg may have understated the matter on Monday, the day before free agency began, when he referred to his new job as a "great challenge."
Even though they have about $14 million in cap room, the Jets didn't make a strong push to keep Keller, Mark Sanchez's favorite target. Keller had been hoping for a long-term deal, but he didn't garner as much interest as expected. He signed with the Dolphins after concluding a two-day visit.
Instead of committing significant money to Keller, the Jets' plan is to start holdover Jeff Cumberland, who caught a career-high 29 passes last season. The Dolphins needed a tight end to replace Anthony Fasano, who signed with the Kansas City Chiefs.
Keller was rebuffed last offseason when he approached the Jets about a long-term extension. There were some rumblings about the franchise tag ($6.06 million), but that never materialized. In fact, there had been little contact between the two sides in recent weeks, a source said.
A first-round pick in 2008, Keller was on the ascent until last season, when he missed eight games due to hamstring and ankle injuries, the first time in his career he missed a game.
Keller finished with career lows for catches (28), receiving yards (317) and touchdowns (two), lousy timing in a contract year. His career yardage total is 2,876, fourth in Jets history among tight ends.
The Jets added another potential starter on offense, signing former Pittsburgh Steelers guard Willie Colon to a one-year, $1.2 million contract, a source said. Brandon Moore and Matt Slauson, last year's starting guards, are free agents, so the Jets were in the market for a low-cost insurance policy.
Colon, released by the Steelers earlier this week, switched to left guard in 2012 after playing right tackle. He played well, but he missed five games late in the year due to a knee injury. Injures have tormented him in recent years. He played only one game in 2010 and 2011, missing the entire '10 season with a torn Achilles' tendon. It will be a homecoming for Colon, who grew up in the Bronx and attended Hofstra.
Garay, 33, had 16 tackles and one sack in eight games with the Chargers last season.
Information from ESPN NFL Insider Adam Schefter was used in this report.