"They substituted the punter as a receiver so we put the punt team in," said Saban, according to Matt Zenitz of AL.com. "Then the QB was still in there. We tried to put the defense back in. I thought they should have given us a little more time to substitute."
Up 48-45 with 1:17 to go, Auburn was facing a fourth down from their own 26-yard line.
In an apparent attempt to keep wideout Jaylen Waddle - who had a 98-yard return touchdown earlier in the game - off the field, head coach Gus Malzahn's team lined up its punter at receiver.
Saban tried to substitute his defense back on but Alabama was flagged for 12 men on the field, giving Auburn a game-sealing first down.
"I really feel it's a pretty unfair play," said Saban.
The six-time national championship winner has led the Crimson Tide to the playoffs in every season since its inception in 2014, but his squad is all but certain to be out of the top four this year.
Alabama's chances of making the CFP fell from 48% to 1.1% after the defeat to its in-state rivals, according to ESPN.