Replays showed that West Brom forward Marc-Antoine Fortune clearly backed into Green, stopping the England goalkeeper from collecting the ball that had looped up in the air off Armand Traore, but ref Chris Foy allowed the goal to stand.
"I've seen the video again and again and it was clearly a foul for their second goal," Cisse told QPR's website.
"He didn't attempt to play the ball. Rob couldn't do anything. It was a clear foul and it cost us dearly.
"We all feel sympathy for Rob. It wasn't his fault. There was nothing he could do. He was clearly fouled.
"Everyone in the stadium was waiting for the referee to award a foul. He didn't, and it's cost us points."