Thomas will receive $9 million, half of the contract, in guarantees.
Thomas' extension follows that of fullback Montell Owens, who signed a three-year extension earlier in the week that will pay him $11.275 million through 2015, with $9.275 million in new money and $4.65 million guaranteed.
The Jaguars can afford to lock up their core players because they started the season $35.4 million under the cap.
A fourth-round choice from the 2009 draft, Thomas was signed through the 2012 season. He's now under contract through 2015.
Thomas is the Jaguars' No. 1 pass catcher this season with 20 receptions for 212 yards and one touchdown.
In 2010 he had 66 receptions for 820 yards and four touchdowns. In 34 career games, the 24-year-old receiver has 134 catches for 1,485 yards and six scores.
Senior writer John Clayton covers the NFL for ESPN.com. Information from The Associated Press was used in this report.