San Francisco 49ers
Following the Grey Cup victory, Garcia was signed as a backup to Steve Young with the San Francisco 49ers of the National Football League. Over the summer, he had been fighting for a spot on the roster, but early in the 1999 season, Young was hit by Arizona Cardinals cornerback Aeneas Williams and suffered his final professional concussion, knocking him out for the year. Garcia stepped in and shared time with former Stanford quarterback Steve Stenstrom finishing the season.
Garcia won his first NFL start against the Tennessee Titans 24–22. After being benched for poor performances, Garcia was reinstated as the starting quarterback and in the final five games of the regular season, finished by tossing 8 touchdown passes to only 2 interceptions. Garcia finished his rookie season with 11 touchdowns and 11 interceptions.
The following season, with Young retired, and despite the 49ers drafting two quarterbacks (Giovanni Carmazzi in the third round and Tim Rattay in the seventh), Garcia kept the starting quarterback position and made his first Pro Bowl appearance. He set a new 49ers' team record with 4,278 passing yards in the 2000 season, although the team finished with a 6–10 record. Garcia finished the 2000 season, his first as a full-time starter with 31 touchdown passes to only 10 INTs. Garcia began the season on a tear, after 7 games, he had thrown for 19 touchdown passes, including 3 games of 4 touchdown passes.
By the 2001 season, Garcia had become entrenched as the 49ers' starting quarterback. He had a career-high with 32 touchdown passes, including 21 over an eight-game span. With Garcia at quarterback, the 49ers made the playoffs, but fell to Green Bay 25–15 in the first round.
2002 saw Garcia's offensive production drop from 31 and 32 TDs in the previous two seasons, to only 21. But even though Garcia's numbers dropped, the 49ers won the NFC West for the first time since 1997, with the division-clinching game coming on a last-second TD pass to Terrell Owens against the Dallas Cowboys. The 49ers trailed the Cowboys 27–17 with under 7 minutes left in the game before Garcia picked apart the Cowboy secondary for 2 touchdown passes (one to Tai Streets and the game winner to Owens). Garcia completed 36 of 55 passes for 276 yards and 3 4th-quarter touchdown passes in the division-clinching win.
On January 5, 2003, during the 2002–2003 playoffs, Garcia led the 49ers to a comeback win over the New York Giants, the second largest comeback victory in NFL playoff history. In the third quarter, the Giants were up 38–14, with about eighteen minutes left to play. Once the 49ers regained possession of the ball, they began a comeback that saw 25 unanswered points, with San Francisco taking a 39–38 lead. The Giants lost an opportunity to retake the lead after a controversial call, and the improbable victory became the signature game of Garcia's 49er career. He threw for 331 yards, 3 touchdowns, 1 interception, and also ran for 60 yards and 1 touchdown.
Garcia's favorite target while with the 49ers was WR Terrell Owens. In 2003, Garcia and Owens's relationship turned sour upon Garcia taking issue with Owens's public praise for the play of backup quarterback Tim Rattay. Garcia responded with a cryptic "we cannot let the sickness spread" remark, prompting Owens to wear a surgeon's mask at the following practice. Following Owens's trade to Philadelphia, Owens was asked in a Playboy interview if he thought Garcia was gay, to which he responded, "If it looks like a rat and smells like a rat, by golly, it is a rat." Garcia called Owens' insinuations "ridiculous" and "untrue."
Following his 2004 trade to Philadelphia, Owens began speaking out and criticizing Garcia for the 49ers' offensive struggles during the 2003 season (the 49ers finished 7–9, with Garcia throwing 18 touchdowns and 13 interceptions during the season).
Garcia revealed on multiple occasions that the pressure of following in the footsteps of Joe Montana and Steve Young had gotten to him.
Upon his departure, Garcia said, "Have somebody step into my shoes and feel what I had to deal with throughout that whole time in San Francisco. The dust would start to settle, and all of a sudden, more fuel was thrown into the fire. It was such a negative situation."
In Owens' first season with Garcia as his quarterback, Owens caught 60 passes and went on to have campaigns of 97, 93, 100 and 80 receptions over the next four seasons, two times leading the league in touchdown catches.
The 2003 season was a disappointment for Garcia and the 49ers. Following their 2002 playoff loss at the hands of the eventual Super Bowl Champion Tampa Bay Buccaneers, the 49ers fired head coach Steve Mariucci and replaced him with former Seattle Seahawks coach Dennis Erickson, who promised a wide open and vertical passing game.
Injuries to key players on both sides of the ball, and the often reckless play of Garcia, took a toll on him, as he missed three games during the season. The 49ers finished 7–9 and missed the playoffs for the first time in three seasons.
Following the 2003 season, Garcia was released.
