The damning statistic at the final whistle was just one shot on target for the visitors and another damaging defeat for Benitez.
Earlier, Atletico trailed at the Vicente Calderon when Aymeric Laporte converted from Benat Etxebarria's corner.
A near post header by Saul Niguez saw Diego Simeone's team level by the half and after visiting pressure left the home side on the back foot, it was a stunning strike from Antoine Griezmann which settled it for Atletico.
Saturday saw an incredible fightback by Deportivo in the Nou Camp, trailing 2-0 with 14 minutes to go after home goals by Lionel Messi and Ivan Rakitic in each half.