Both coaches were released as New Orleans head coach Sean Payton confirmed he plans on switching to a 3-4 defense for next season.
"I personally want to thank Steve and Ken for their contributions during what was an unprecedented 2012 season," Payton said. "Philosophically we are changing our defense to a 3-4 alignment and right now is the best time to accomplish this transition."
The Saints were ranked the worst team in opposing rushing yards per game (292.6) and second-worst in passing yards per game (147.6) last season.
Spagnuolo served just one season with the Saints, after three seasons as head coach of the Rams. He was 10-38 during his tenure with the St. Louis, including a league-worst 2-14 in 2011-12. He also roamed the sidelines as the defensive coordinator for the Giants in 2007-08.
Flajole also served just one season with the Saints, after three years as defensive coordinator of the Rams.