The Basque trainer put the loss down to the dismissal of Sofiane Feghouli on the hour mark, as he felt the incident shot down any chance Los Che once had of picking up points
Ignacio Camacho scored the only goal of the game in the first half to tie Manuel Pellegrini's side level on points with Los Che in third place, but according to the 40-year-old, the turning point of the contest came midway after the break when the former Grenoble starlet was given his marching orders.
"The team failed after going a man down," Emery told reporters after the match.
"The goal gave [Malaga] peace of mind. They began to feel comfortable and did not have to tighten their grip on the match.
"It is a bad defeat, but a just result on the scoreboard."
Emery insisted that he put his team out with the hope that they would leave La Romareda with all three points, but added allowing Malaga back into contention for a Champions League qualifying spot is his biggest regret.
"We played with the intention of winning, but if we couldn't achieve that, then a draw would not have been bad," he continued.
"Worst of all, we have now left Malaga fighting with us for third place, but fortunately it's still in our hands."