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, Steve Young was sacked by
Aeneas Williams and suffered his final professional concussion, knocking him out for the year. Garcia stepped in and finished the season.
The following season, with Young retired, 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. In both of the next two seasons, Garcia led the 49ers to the
playoffs.
Garcia had 31 and 32 passing touchdowns in the 2000 and
2001 season seasons, more than any other quarterback over those two seasons. As one of the top quarterbacks in the league, Garcia went to the Pro Bowl in three consecutive seasons (2000-2002).
On
January 5, 2003, during the
2002-2003 playoffs, Garcia was a large part of the 49ers' comeback win over the
New York Giants, the second largest comeback victory in NFL playoff history. In the game's third quarter, the Giants were up 38-14, with about 18 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.
Following a disappointing
2003 season, in which Garcia was hampered by back problems, the 3-time Pro Bowler was released by the 49ers due to
salary cap issues. Garcia also had a falling out with wide receiver
Terrell Owens, who blamed Garcia's lack of arm strength for holding Owens back.
Shortly after his release, on
January 14, 2004, Garcia was arrested for a
drunk driving violation in
San Jose, after attending a
San Jose Sharks game, by the
San Jose State University Police Department.