Falcons general manager Thomas Dimitroff made the announcement late Wednesday night.
"We have had continued dialogue all offseason with Julio and his representation," Dimitroff said in a statement. "We have come to an agreement with Julio, and we will re-address everything in 2019. I appreciate everyone's hard work and communication on this. ..."
Jones, 29, was originally going to skip camp. The Falcons previously said that they would not adjust the deal for Jones.
Jones was set to make $10.5 million in 2018 in the third season of a five-year, $71.25 million contract extension he signed in 2015. Terms of the new 2018 contract were not immediately known.
Jones elected against participating in the Falcons' voluntary offseason program and did not attend the team's mandatory minicamp. He attended quarterback Matt Ryan's passing camp with other teammates, however.
Jones is coming off another huge season with 88 receptions for 1,444 yards, although he only reached the end zone three times.
It marked the fourth consecutive season in which Jones amassed at least 1,400 yards receiving and the fifth time in seven campaigns that he has eclipsed 1,000 yards.
Jones has appeared in 95 regular-season games for the Falcons, recording 585 catches for 9,054 yards and 43 touchdowns since being selected with the sixth overall pick of the 2011 NFL Draft.