The ruling prompted more than 100 lawmakers to support a parliamentary initiative that could have paved the way for proceedings to impeach Gibran.
Budi Arie said the letter was submitted directly to Prabowo on Wednesday.
Having studied in Singapore and Australia, Gibran had used an Indonesian equivalence certificate to demonstrate his educational credentials.
He was 36 at the time, below the minimum age requirement of 40 for candidacy.
He became eligible only after a controversial ruling by the Constitutional Court exempted him from that age requirement.
At the same time, a free school meals programme is struggling for funding.
Parts of Indonesia have recently battled the country's worst wildfires in a decade.
The national stock market faces crisis amid allegations of widespread market manipulation.
All of this is unfolding at a particularly turbulent period in Prabowo's presidency.