Babineaux was drafted by the Atlanta Falcons in the second round with the 59th overall pick of the 2005 NFL Draft. On November 25, 2008, he signed a five-year contract extension with the Falcons. In 2009, he had nine tackles and 2.5 sacks against the Washington Redskins. He had a career-high six sacks in 2009, which led all NFL defensive tackles. In 2010, he posted 31 tackles, one interception, two forced fumbles, and one fumble recovery, which was returned for a touchdown against the Seattle Seahawks. In the 2011 season, he recorded 21 total tackles and one sack.