Atkinson gave Juan Mata Chelsea’s second goal when replays showed the ball hadn't crossed the line.
Adebayor could not hide his anger after the game, telling Sky Sports News: "To be honest, we have to blame the referee.
"I think we have done well and he has made a lot of mistakes and made a lot of wrong decisions.
"We are all disappointed. But what do you want me to tell you?
"How many goals scored this season were disallowed that were onside?
"To be honest, I'm just tired of it and everyone is talking about goal-line technology.
"They have to make something happen because it's killing the league, it's killing the FA Cup, it's killing the game, it's killing everything."