San Francisco 49ers
Davis was selected sixth overall in the first round of the 2006 NFL draft by the San Francisco 49ers. He joined Kellen Winslow Jr. as the fourth highest tight end ever drafted after Ron Kramer, (Green Bay, fourth overall in 1957) Mike Ditka (Chicago, fifth overall in 1961), and Riley Odoms (Denver, fifth overall in 1972). Davis was the top tight end prospect in the 2006 NFL Draft, partially due to a strong performance at the scouting combine. He ran the 40-yard dash in 4.40 seconds. Davis also broad-jumped 10'08", nearly a foot farther than the next-best tight end, Marcedes Lewis.
Vernon's first reception in the NFL was a 31-yard touchdown catch from quarterback Alex Smith, against the Arizona Cardinals on September 10, 2006. Smith added a career-long 52-yard touchdown against the Green Bay Packers on December 10 with a short catch followed by a long run. Davis missed six games due an injury he suffered on September 24, 2006. Davis sustained a hairline fracture to his left fibula, on a non-contact play against the Philadelphia Eagles, but returned on November 19 against the Seattle Seahawks.
Davis finished his rookie year with 20 receptions for 265 yards and three touchdowns in 10 games and eight starts.
During Week 3, Davis was injured while attempting to catch a pass from Smith against the Pittsburgh Steelers. Davis sprained his right knee and missed the next two games. Despite his injury and the 49ers' offensive ineptitude, Davis bettered most of the numbers from his rookie season. Even though his yards per reception diminished, Davis finished his second professional season with 52 receptions for 509 yards and four touchdowns in 14 games and starts.
In October 2008, after catching a seven-yard pass in the third quarter against the Seahawks, Davis slapped Seahawks safety Brian Russell in the facemask, resulting in a 15-yard penalty, causing head coach Mike Singletary to bench Davis and then send him to the locker room for the rest of the game. After the game, Singletary then spoke his famous "I want winners" rant. This resulted in Davis changing his attitude from himself, to the team. In the next game against the Arizona Cardinals, Davis leaped over a defender and caught a pass from quarterback Shaun Hill resulting in a touchdown, his first of the season.
Davis finished the season with 31 receptions for 358 yards and two touchdowns in 16 games and starts.
Through Week 11 of the 2009 season, Davis led the NFL with nine touchdown receptions, tied with wide receivers Larry Fitzgerald and Randy Moss. In the final game of the regular season, he tied the all-time record for most touchdown receptions for a tight end in a single season with 13, sharing the record set by Antonio Gates of the San Diego Chargers in 2004; that record stood until 2011, when it was broken by Rob Gronkowski of the New England Patriots. Davis was selected to appear in his first Pro Bowl after recording 78 receptions for 965 yards and 13 touchdowns in 16 games and starts.
Before the 2010 season, Davis was awarded a five-year contract extension for $37 million with $23 million guaranteed. The deal made him the league's highest paid tight end. During a Week 6 17–9 victory over the Oakland Raiders in Week 6, Davis recorded his third straight game with a touchdown.
Davis finished the 2010 season with 56 receptions and 914 yards and seven touchdowns in 16 games and starts. He was ranked 88th by his fellow players on the NFL Top 100 Players of 2011.
In 2011, Davis had 67 receptions for 792 yards with six touchdowns in 16 games and starts, helping the 49ers win the NFC West division and make the postseason for the first time since 2002. In the playoffs in the Divisional Round against the New Orleans Saints, he had seven receptions for 180 yards, breaking Kellen Winslow's record (166) for most yards by a tight end in a playoff game. Davis scored two touchdowns, and on the game-winning drive, he had a critical 47-yard reception that put the 49ers in a position to tie the game. With nine seconds remaining, Davis caught the game-winning touchdown pass from Alex Smith, now referred to as "Vernon Post" or "The Catch III". Davis caught three passes for 112 yards and another two touchdowns against the New York Giants in the NFC Championship, but the 49ers lost 20–17 in overtime. He was ranked 43rd by his fellow players on the NFL Top 100 Players of 2012.
During the 2012 season, Davis caught 41 passes for 548 yards and five touchdowns in 16 games and starts.
During the NFC Championship Game, Davis recorded five receptions for 106 yards and a touchdown in the 28–24 comeback victory over the Atlanta Falcons. During Super Bowl XLVII, he had six receptions for 104 yards in the 34–31 loss to the Baltimore Ravens. Davis was ranked 38th by his fellow players on the NFL Top 100 Players of 2013.
Davis began the 2013 season much like the 2012 playoffs ended: as a trusted and reliable target for quarterback Colin Kaepernick, catching his first touchdown pass of the season in the first quarter of the first game, at Candlestick Park on September 8, 2013, against the Green Bay Packers. Davis finished the 2013 season with 52 receptions for 850 yards and 13 touchdowns in 15 games and starts.
Davis added two touchdown receptions in the playoffs, one coming against the Green Bay Packers in a Wild Card Round victory, and another in a Divisional Round victory over the Carolina Panthers. He was named to the Pro Bowl. Davis was ranked 51st by his fellow players on the NFL Top 100 Players of 2014.
In 2014, Davis had 26 receptions for 245 yards and two touchdowns, both of which occurred in the season-opening 28–17 road victory over the Dallas Cowboys. He was dealing with ankle and back issues, which hindered him most of the time during the season.