Wenger was livid on the touchline as Juan Mata fired the home side ahead moments after Ramires appeared to foul Francis Coquelin. The Frenchman's mood was not improved when Gunners goalkeeper Wojciech Szczesny was adjudged to have brought down Ramires in the box, claiming the Brazilian should have been booked for diving.
Wenger said: "The referee gave a lot of free-kicks today, and some much less than the Coquelin one. It's frustrating. It doesn't mean we should have conceded the goal but, in the big games, these decisions have big implications."
Admitting he was "surprised" Atkinson did not send off Szczesny after penalising him for a last-man foul, Wenger added: "He could have given Ramires a yellow card as well."
However, Wenger refused to absolve his players from blame for the defeat, the second league game in succession in which they were made to pay for a slow start after last weekend's loss to Manchester City.
"We had a similar start to Man City last week, didn't defend too well and gave them too much incentive," he said. "We didn't play well in the first half, but we were much more dangerous in the second half, with a different attitude. Unfortunately we didn't make enough of our corners, free-kicks and the chances we created. That's why we lost the game.
"It's very damaging for our position in the league and difficult to swallow."
Chelsea interim manager Rafael Benitez insisted it was not only his players who benefited from controversial decisions as he finally broke his 2013 home hoodoo.
Claiming the European champions were denied a second penalty, he added: "We deserved to win. The team were doing really well. You can analyse every incident.
"The team were very good in the first half, and defended with character in the second half."