The procedure was performed by renowned foot surgeon Dr. Robert Anderson, who previously repaired multiple fractures to Jones' right foot.
Jones faces a 4-5 month recovery to fully heal, according to the team. The Falcons expect him to be ready for training camp in July.
Falcons coach Dan Quinn said last week there was a possibility Jones would undergo surgery after meeting with Anderson. The timing of the procedure means Jones should be recovered in time for offseason workouts and minicamp.
The injury nagged Jones throughout the 2016 season and caused him to miss two games. His game and practice reps were limited late in the regular season, and the Falcons also were cautious with Jones during the postseason.
Jones still finished with 1,409 receiving yards, second behind T.Y. Hilton of Indianapolis (1,448) but in two fewer games than Hilton. Jones caught 83 passes and six touchdown passes, tied for the team lead with Taylor Gabriel.