On Friday, the 49ers showed they want to keep control of Smith's contract, exercising his 2015 option worth $9.75 million. Until next March, the option is only guaranteed if Smith suffers a major injury in 2014 that would affect the 2015 season. The 49ers also could pull the option before the end of the 2014-15 league year in March, or they could trade Smith.
The 49ers had until midnight ET Friday to make the decision.
Had the 49ers not exercised the option, Smith, 24, would have been set to become a free agent after the 2014 season. If the 49ers had decided not to pick up the option and then placed the franchise tag on Smith instead next winter, his 2015 salary would have increased to the $12-13 million range.
Because of that, it was widely considered the smart football move for the 49ers to exercise the option.
Asked last week if he hoped Smith would play for the 49ers the next two seasons, Baalke replied: "And in 2016 and 2017 and 2018 ... You don't just open the door and toss people out."
Smith was arrested at Los Angeles International Airport on April 13 for making a fake bomb threat, and officials in L.A. are considering misdemeanor charges. Smith also will face felony gun charges and a drunken driving charge at a Santa Clara County courthouse May 12. Smith may face an NFL suspension based on the outcome of his legal cases.
The fifth-year option was part of the 2011 collective bargaining agreement. Smith was the No. 7 overall pick that year.
The team is not expected to exercise its option on another of its 2011 first-round picks, QB Blaine Gabbert. The 49ers acquired Gabbert, the No. 10 overall pick that year, from Jacksonville in March for a sixth-round pick.