The new deal is worth $31 million over four years with $17.5 million guaranteed.
Last season, the former UCLA product gained 824 yards on 197 carries and added 62 catches for 565 yards.
He scored 14 touchdowns, and in 2009, is expected to carry the load following the release of Fred Taylor, the franchise's all-time leading rusher, in February.
"It's an opportunity to reward one of our own," said General Manager Gene Smith on the team's Web site.
Since he was picked in the second round of the 2006 NFL draft (28th overall), Jones-Drew has 530 carries for 2,533 yards with 34 touchdowns and 148 receptions for 1,408 yards and four touchdowns.
"We believe he's the feature guy and it's his time," Coach Jack Del Rio told the Florida Times-Union.