He played college football for the Iowa Hawkeyes and was selected by the Falcons in the second round of the 2005 NFL draft.

[8] Babineaux started all 16 games in the 2012 season and recorded 3.5 sacks, 31 total tackles, and one interception.

[14] At the end of the 2016 season, Babineaux and the Falcons reached Super Bowl LI, where they faced the New England Patriots on February 5, 2017.

In the Super Bowl, he recorded one assisted tackle as the Falcons fell in a 34–28 overtime defeat.

[16] Jonathan is the older brother of former Seattle Seahawks and Tennessee Titans safety Jordan Babineaux.