"Justin's All-Pro contributions on the field, as well as his leadership on and off the field, are integral to our success as a team," general manager Trent Baalke said in a statement. "Justin consistently sets a standard of excellence, serving as an example for everyone within our organization. This contract allows Justin to finish his career as a 49er!"
Just last week, the 33-year-old Smith had told reporters that he was resigned to playing out the season and facing the possibility of having to sign elsewhere in 2014 if he wanted to continue his career.
"I wanted to be here. That makes it simple," Smith said Wednesday. "They wanted me to be here, and I wanted to be here, so that makes it easy."
Smith underwent surgery on a partially torn left triceps muscle shortly after the team's 34-31 Super Bowl loss to the Baltimore Ravens.
The defensive tackle suffered the injury on Dec. 16 against the Patriots and missed the final two games of the regular season, ending his streak of 185 consecutive starts. He played with the injury during the playoffs while wearing a bulky brace, however, and made 12 tackles during the 49ers' Super Bowl run, including three against the Ravens in San Francisco's title-game loss.
"The good news is it's healed. It's close to 100 percent for what I want it to be," he said Wednesday. "I feel good about it, feel confident about the season. I've never been injured like that. I didn't know anything with the rehab process, what to expect, what coming out of surgery would be like. It's all been really good."
Smith has made the Pro Bowl four straight seasons. Since joining San Francisco in 2008, he has 536 tackles, 32 sacks, seven forced fumbles, four fumble recoveries and one interception.
Information from The Associated Press was used in this report.