Thomas was drafted by the Jacksonville Jaguars in the fourth round of the 2009 NFL Draft. As a rookie he started four of the 14 games in which he played, and had 48 receptions for 453 yards and a touchdown. His 48 receptions were tied with Michael Crabtree for fourth among all rookies.
A key play of his career was in a 2010 Week 10 game against the Texans. With just 3 seconds remaining in regulation and the game tied at 24, QB David Garrard launched a "Hail Mary" pass from the 50-yard line intended for Mike Sims-Walker. The ball was batted down at the goal line by Texans DB Glover Quin, and then hit Thomas in the chest. Thomas was able to grab the ball next to his left knee before it hit the ground, and he took a step forward into the end zone for the game-winning touchdown.