Balogun, the American leader with three goals, received a red card for stepping awkwardly on the right ankle of Tarik Muharemovic of Bosnia and Herzegovina in a 2-0 round of 32 win on Wednesday (Thursday AEST). A red card triggers an automatic one-game suspension.
FIFA announced on Sunday (Monday AEST) the suspension had been lifted, triggering praise from Trump.
The move sent shockwaves around the football world, sparking outrage from Belgium and concern from England manager Thomas Tuchel, who pondered whether the "strange" decision opened a can of worms in that other teams may now start appealing red and yellow cards dealt through the tournament.
Former England great Wayne Rooney went further, labelling the move "disgrace" and saying FIFA "should be ashamed" of itself.
Trump called FIFA president Gianni 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 as they were not authorised to speak publicly about the matter.
"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."
Garcia wouldn't respond when asked about a possible appeal to the Court of Arbitration for Sport.
"In order to safeguard the legitimate rights of all participating teams and to protect the fundamental principles of fair play in our sport, both at this FIFA World Cup and at future editions of the tournament, the RBFA is investigating all potential options," the Belgian federation said in a statement.
Balogun's red card had been one of the World Cup's most controversial and consequential decisions.
"If you look at the foul, it was just zero intent at all," US star Christian Pulisic said. "I felt like there was much worse ones that went on this tournament."
The US Soccer Federation learned of FIFA's action in a message sent by FIFA in its portal on Sunday morning.
"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.
However, Tuchel said FIFA's move set a dangerous precedent, commenting 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?"
While opining Balogun didn't deserve a red card, Tuchel said the referee and VAR had made their decision.
"Who overturns this decision and when and on what grounds? And how far does this go now? It's just strange for me. We just want to have consistency in the decisions," he said.
"So, is our yellow card after the first minute against Declan Rice … we can now debate endlessly. I think it is not a yellow card. Do we get this back?"
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."
FIFA in November deferred the final two games of a three-match ban for Portugal's Cristiano Ronaldo for a red card against Ireland in a World Cup qualifier, allowing him to play at the start of the World Cup.
- With PA
