As a junior in 2012, he started all 13 games at safety and finished third on the team in tackles with 91 (42 unassisted), two interceptions, and seven pass breakups. He was recognized as a consensus first-team All-American, having received first-team honors from the American Football Coaches Association, Football Writers Association of America, ESPN, and Scout.com, and second-team honors from the Associated Press, Walter Camp Football Foundation, Athlon Sports, CBSsports.com, and Sports Illustrated. He was also a first-team All-SEC selection.
Reid entered the 2013 NFL Draft. The San Francisco 49ers traded up with the Dallas Cowboys to hold the 18th overall pick. He was drafted 18th overall by the San Francisco 49ers, because former safety Dashon Goldson left via free agency to the Tampa Bay Buccaneers.
On August 27, Reid won the team's starting free safety job over teammate Craig Dahl. In his first regular season game as a 49er, a week 1 win against the Green Bay Packers in San Francisco, Reid recorded his first NFL Career interception on a pass thrown by Aaron Rodgers. In the following game against the Seahawks, he recorded another interception. However, in that game, he sustained a concussion. In one of his best games of the year, Reid notched an interception and recovered a fumble against the Arizona Cardinals. Later in the season, against the Carolina Panthers, he was concussed again. However, in his whole rookie season he did not miss a start. He ended his rookie season with 77 tackles, and 4 interceptions. At the end of his terrific rookie season, Reid was elected to the 2014 Pro Bowl.