Flynn, obtained by the Raiders from Seattle in April in exchange for a 2014 fifth-round draft pick, was cut loose after Terrelle Pryor emerged as Oakland's top signal-caller in the pre-season.
"Terrelle came in and he took over the job," Coach Dennis Allen told the San Jose Mercury-News. "He's earned the position that he's in. So, we just felt like it's probably best to move on from that."
Flynn is owed $6.5 million from Oakland for 2013.