The deal, first reported Thursday night by ESPN.com, was contingent upon Winborn, 26, passing a physical examination, which he did. The fifth-year veteran arrived in Jacksonville late Thursday night and the physical was administered on Friday morning.
"It's exciting," Winborn said when reached on his cell phone. "It's a new start for me."
The trade ends a strange chapter in the career of the former Vanderbilt star.
Winborn has suffered a series of injuries that slowed his advancement at times. The most serious was a neck injury in 2003. There have also been knee and shoulder injuries. It is likely that the neck injury received the most scrutiny from Jacksonville team doctors.
To create a roster spot for Winborn, the Jaguars released defensive tackle Martin Chase.
"It was an opportunity to acquire a linebacker who's a good player and fits our system," Jaguars coach Jack Del Rio said. "It wasn't anything that was too costly or too difficult to pull off."
Del Rio wouldn't commit to Winborn becoming a starter when he begins workouts with the Jaguars next week, but said he would get a spot with the club's special teams.
"We see him as a guy who's played well, has started, so he has experience, has speed and can help us on [special] teams," Del Rio said. "We'll let him grow into a role."
San Francisco first-year head coach Mike Nolan last week told Winborn to clean out his locker and leave the team, and then announced that the 49ers would attempt to trade him. The decision came after Winborn, who started the first two games of the season, was demoted in favor of Andre Carter, a one-time first-round defensive end who was moved to linebacker in Nolan's new 3-4 alignment.
Nolan acknowledged that, while Winborn told him he did not feel he was a backup, there was no verbal confrontation. Neither did Winborn, both Nolan and the player said, ask to be traded. Apparently the decision to deal Winborn was made by Nolan because he felt it would be in the best interest of both parties.
Late last week, Nolan said there were four teams that had indicated interest in a trade but Jacksonville, at least at the time, was not believed to be one of those franchises. One of the teams that pursued a deal is Seattle, and it is believed that New Orleans also showed some interest.
A second-round choice in the 2001 draft, Winborn has appeared in 43 games, mostly as a weakside linebacker in a 4-3 defense. He has 258 tackles, 8½ sacks, three interceptions, four forced fumbles, three recoveries and 16 passes defensed. A versatile defender, he had his best season in 2004, registering 104 tackles and 4½ sacks. In his three games in 2005, Winborn had 13 tackles.
While it is believed that some adjustments were made to his contract to accommodate the trade, Winborn, who was paid by the 49ers even during his absence from the team, will earn the full $1.75 million he is due for this season. Under terms of the contract, Winborn is signed through 2009, at base salaries of $3 million and roster bonuses of $3 million for each of the next four years.
That is only a formality, though, since Winborn has already reached performance levels that allow him to void the final four years of the contract and to become an unrestricted free agent next spring.
Len Pasquarelli is a senior NFL writer for ESPN.com. To check out Len's chat archive, click here. The Associated Press contributed to this report.