According to a source, Tomlinson won't take a pay cut from $6.725 million but did restructure his deal to give the team a cap break in 2009. Tomlinson's cap number was scheduled to be $8,791,666.
General manager A.J. Smith sounded relieved that any uncertainty over LT's future was over.
"The way I'm looking at it, LT has helped us on the field and now he's gone a step further and he's helped us off the field," Smith told The Associated Press.
"I'm just happy that it worked out," Smith said. "I felt comfortable that it had a chance. We wanted him back, he wanted to come back. Everything was as smooth as it can be in negotiations."
Tomlinson will receive an unspecified guaranteed amount of money in 2010, the source said. The amount might not be large enough to guarantee Tomlinson's place on the team, but it gives him some security for the 2010 season.
Tomlinson reduced his salary in 2010 and 2011. He was scheduled to make $8 million next year and $9.275 million in 2011. The final three years of his old contract were worth $24 million.
"This is a good day for the Chargers and for Chargers fans," owner Dean Spanos said. "It was important for me to get this done so LT could continue his career here in San Diego where he means so much to our team, our fans and our community. The alternative was just unthinkable. He belongs in San Diego."
Tomlinson said, "I love San Diego and being a part of this team with my teammates. My No. 1 priority was to stay here in San Diego. I truly believe this is the place that gives me the best chance to be successful and win a championship. I want to finish the job we started when I got here eight years ago. My heart has always been in San Diego. I couldn't imagine putting on another uniform.
"I really appreciate the role Dean played throughout this process. He made it work for everyone and I appreciate his friendship more than he knows."
Tomlinson was slowed during the regular season with a toe injury, then hurt his groin in the season finale. He was forced out of an overtime playoff win against the Indianapolis Colts and sat out against the Steelers, the first game he'd missed due to injury in his brilliant eight-year career.
It was the second straight year his postseason was cut short by injury. That, coupled with the fact Tomlinson turns 30 this summer, raised questions about how long he would be a Charger. The team said it needed salary-cap relief in order to sign other players to contract extensions, and it zeroed in on Tomlinson's deal.
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Tomlinson's salary-cap number would have been $8.8 million in 2009, including a prorated share of the signing bonus from his 2004 contract.
While his 1,110 yards rushing were the lowest of his career, Tomlinson still finished fourth in the AFC and 10th in the NFL.
The new deal came three weeks after the Chargers put the nonexclusive franchise tag on Darren Sproles, virtually assuring the speedy little running back/returner will be back next season. If Sproles and the Chargers don't negotiate a long-term deal, he'll make $6.62 million next year.
"We have cap relief, and now we have the opportunity over the next couple of years to address some things we'd like to get done," Smith said. "I'm just glad this has passed by and we can move on with a lot of things we need to do."
Smith would like to see Tomlinson's career culminate with a long-sought Super Bowl title.
"It would be a really, really wonderful way to cap it off for a great player," Smith said. "We know he's a Hall of Famer waiting to go. All I know is he's done everything he can on his end, and I need to pick up my end of the deal and get it done.
"I know what he's done over the years, and obviously we've got to help him, too," Smith said. "We need to shore up that front line and establish a dependable ground game."
This saga has had a few twists and turns.
Smith was livid that the severity of Tomlinson's groin injury was revealed several hours before the playoff game against the Colts, leading him to call out the player and his agent, Tom Condon.
Tomlinson, long the franchise's most brutally honest employee, confirmed he had a detached tendon in his groin while the team said only that he had a strained groin.
In late January, Smith mocked a statement Tomlinson posted on his Web site, in which he said he wanted to stay in San Diego, mimicking the star's comments practically word for word. Smith later said he regretted making the comment.
Tomlinson was voted the NFL MVP in 2006, when he set league records with 31 touchdowns -- 28 rushing -- and 186 points. He also won the first of two straight league rushing titles with a career-high 1,815 yards.
A five-time Pro Bowler, Tomlinson owns or shares 28 team records. The NFL's 14th all-time leading rusher with 11,760 yards, he ranks second all time in rushing touchdowns (126) and is tied for fourth in total touchdowns (141).
He was the NFL's Walter Payton Man of the Year in 2006 for his work in the community.
Senior NFL writer John Clayton and The Associated Press contributed to this report.