Jacksonville announced the transaction on Friday. The Jaguars placed fourth-year offensive lineman Josh Wells on injured reserve in a corresponding move.
The Giants placed Flowers on waivers on Tuesday and signed tackle Brian Mihalik off the practice squad. Flowers, 24, was the No. 9 overall pick in the 2015 NFL Draft. The 6-foot-6, 334-pound tackle appeared in 51 games from 2015 through 2018. He appeared in five games this season, making two starts at right tackle.
Flowers played with Jaguars offensive lineman Brandon Linder at the University of Miami.
"You always hate to lose teammates," Giants quarterback Eli Manning told reporters on Monday.
"Ereck, he's competed his tail off. He's fought, he's been through a lot, adversity. I appreciate everything he's done. I appreciate the way he's played hurt and handled a tough situation. Even these last weeks, when you're told someone else is playing, he's done everything we've asked him to do. I hate to lose a teammate."
Giants coach Pat Shurmur said Flowers' time with the Giants had "run it's course."
"We appreciate Ereck's efforts, and we just wish him the best," Shurmur told reporters. "Sometimes a change of scenery is good for a person, and we're just hopeful he can go out and continue to have a good career."
The Jaguars face the Dallas Cowboys at 4:25 p.m. on Sunday in Arlington, Texas.