Luis Suarez took a quick free kick after being fouled by Barcary Sagna as the Reds broke, ending with an easy tap-in for Henderson.
But Atkinson pulled the play back in order to award a yellow card to the Arsenal defender.
"That was a poor decision," said Rodgers. "I think you've got to let the game flow. If that's the ruling, then it's not a ruling that is very good.
"We're always asking players to be honest and get up and play, not roll about on the floor, and if they are going to be discouraged from doing that then they might stay and roll about, try to get someone a yellow card.
"I got an explanation from the fourth official on it, and it is disappointing, to be honest.
"He said it was the next phase of the game, so he was given a yellow card, and it could only have been given at that point.
"I thought it was a poor decision because you have to let the game flow, but that was the reason he gave it. It was clever play (from us), and we got a goal from it."
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