UEFA said in a statement on Monday that FIFA "crossed a red line" with its decision not to enforce Balogun's mandatory one-game ban, which is understood to have come after a phonecall from US president Donald Trump to FIFA boss Gianni Infantino.
FIFA's ruling on Sunday to defer Balogun's ban for one year of probation shockingly deviated from soccer's traditional rule of law and drew stinging criticism globally, including from former World Cup stars and coaches at this tournament.
"It's a bad, bad, bad, bad, bad decision that will hurt the World Cup," Norway coach Norway coach Stale Solbakken said of the move, which allows Balogun to play in Monday's (Tuesday AEST) last 16 match against Belgium.
England boss Thomas Tuchel said the "strange" decision risked opening a can of worms in that other teams may now start appealing red and yellow cards dealt through the tournament.
And former England great Wayne Rooney went further, labelling the move a "disgrace" and saying Infantino "should be ashamed".
UEFA, whose member federations include Belgium, insisted: "Sometimes rules are open to interpretation. In this case not.
"When the certainty of rules is no longer guaranteed by its guardians, the integrity of the game is at stake and the credibility of a competition is undermined.
"We express our disbelief at such an unprecedented, incomprehensible and unjustifiable decision."
The Belgian soccer federation was preparing an appeal in Seattle in the early hours of Monday to challenge the Balogun ruling before a FIFA-appointed appeals judge. The game against the US is due to kick off at 5pm local time.
Balogun, the American leader with three goals, received a red card for stepping on the right ankle of Tarik Muharemovic of Bosnia and Herzegovina in a 2-0 round of 32 win on Wednesday.
While a red card triggers an automatic one-game suspension, FIFA announced on Sunday the suspension had been lifted, triggering praise from Trump.
Trump called Infantino after the game asking that FIFA review the red card, according to a person familiar with the call who spoke on condition of anonymity.
"Thank you to FIFA for doing what was right, and reversing a great injustice!" Trump said in a statement on social media.
The Royal Belgian Football Association (RBFA) said it was "astonished" and Belgium coach Rudi Garcia mocked FIFA's action.
"I didn't know that in the offices of FIFA the 5th of July was the 1st of April in Europe," Garcia said through a translator in an April Fools' Day comparison.
"The Belgian federation does not defend itself, it does not protect the national team. She defends football in general, she defends her integrity, her ethics. I think it's the first time in the history of the World Cup that there is this kind of decision."
Balogun's red card had been one of the World Cup's most controversial and consequential decisions - and was made more so by FIFA's action.
"The implementation of the match suspension is suspended for a probationary period of one year," FIFA announced, adding Balogun's ban would be enforced if he committed an infringement of a similar nature in that period.
FIFA said its decision relied on Article 27 of disciplinary committee rules.
"The judicial body may decide to fully or partially suspend the implementation of a disciplinary measure. By suspending the implementation of the sanction, the judicial body subjects the person sanctioned to a probationary period of one to four years," the rule states.
Tuchel voiced his dismay after a 3-2 win over Mexico in which England's Jarell Quansah was sent off.
Put to Tuchel there might be hope Quansah can play in England's quarter-final against Norway given Balogun was cleared, the German said: "Where does this start and where does this end now?
"Can we overturn it or not overturn it? What's going on? Where to draw the line is the question that I ask.
"Do we appeal if a yellow card is not a yellow card? Do we think it is not a red card or who thinks it?"
Speaking on the BBC, Rooney said: "For this to be suspended, they either take the red card away which is probably the right decision and then he can play. But to suspend it for a year? I think it's an absolute disgrace. Infantino should be ashamed of this."
