Michael Essien has escaped any further disciplinary action following his tackle on Bolton defender Tal Ben Haim.
Referee Rob Styles, after reviewing footage, said he should have given a red card to the Chelsea midfielder.
But Fifa stepped in to prevent retrospective punishment as Styles saw the incident at the time and deemed a yellow card sufficient punishment.
The Football Association consulted Fifa and were told that the decision could not be reversed.
Fifa has previously expressed concern following an incident at the start of the season when a red card that was shown to Jermaine Jenas, then of Newcastle, was subsequently downgraded to a booking.
"The FA sought clarification from Fifa whether any additional disciplinary action could be taken," the FA said in a statement.
"Given that the referee had seen the incident involving Essien and decided to show a yellow
card, Fifa made it clear to the FA that in such cases the referee's decision is final and cannot be changed retrospectively."
Bolton boss Sam Allardyce had expressed shock at the original decision and said the player feigned injury to escape dismissal.
But Blues boss Jose Mourinho was quick to dismiss those claims and when quizzed on whether he thought Essien was play-acting said: "Of course not. You can say that for sure.
"He's a fair player and a player with an incredible record on disciplinary issues. He is a very clean player."
Bolton were leading 1-0 at the time that the Ghanaian international clattered into the Israeli, catching him high on his shin.
The Trotters eventually lost 5-1 and Allardyce described Essien as "very, very clever".
"I am shocked he was not sent off but Essien went down as if he was injured himself," he said after the match.
"He knew it was a bad tackle, of course he did. We all knew - apart from the referee, unfortunately. He booked him but he knows it should have been a red.
"We went down to 10 men with the score at 2-1, whereas Chelsea should have been 1-0 down and down to 10 men.
"I could have been the first manager to beat Chelsea this season. It has been a major influence on the result."