FAT chief and FIFA executive committee member Worawi Makudi was forced to postpone the presidential elections indefinitely due to the court injunction after Pattaya FC filed a case.
The argument centres on a FIFA-backed reform that would slash the number of eligible voters from around 180 to 72.
FIFA warned of a possible suspension should Pattaya not drop the claim by Monday, which Worawi said would jeopardise lucrative upcoming tours to Thailand by Barcelona, Manchester United, Liverpool and Chelsea.
"Pattaya has gracefully agreed to abide by the FIFA directive and has withdrawn the case from the court," Worawi told Reuters in a statement. "The matter is hereby resolved."
Worawi, 61, who failed to become Asian Football Confederation president in May, wanted to push through the new reforms before holding the election, just before his latest term ended.
Critics said that shrinking the vote was a ploy by Worawi to retain his seat amid growing unpopularity but he defended his action, saying the reforms were a FIFA requirement.