Several media reports last week said the team and Pendergast had parted ways, but the Cardinals did not confirm his firing until Saturday through a statement from Coach Ken Whisenhunt.
Pendergast, 41, had held the post since 2004 when he was hired by former head coach Dennis Green.
Arizona finished the 2008 regular season 28th in the NFL in points allowed (426) and 19th in yards allowed.
"Clancy is a talented coach and we appreciate all that he's contributed in his time with the Cardinals," Whisenhunt said. "I took a look at the last two years as a whole and felt this move was necessary to help us continue the progress we've made."
Pendergast's firing means Whisenhunt has lost his top two coordinators since the Cardinals were beaten by Pittsburgh 27-23 in Super Bowl XLIII last Sunday.
Offensive coordinator Todd Haley was named head coach at Kansas City Friday.