Jones will make $10.176 million in 2015.
Jones, 25, injured his foot in Week 5 of last season and missed the remainder of the 2013 campaign. He caught 41 passes for 580 yards and two scores before getting hurt.
The Falcons have said Jones, the sixth overall draft pick in 2011 out of Alabama, would participate in offseason workouts on a limited basis.
In three seasons, Jones has 174 catches for 2,737 yards and 20 touchdowns.