The former South Korean assistant coach, who took the reins of the Reds in August 2007, handed in his notice earlier in the week, claiming that he had been let down by the club.
"When I came back to Iran, Persepolis authorities made lots of promises to provide me with good conditions but most of these promises were not kept," Ghotbi said.
"My resignation is the most painful decision I have ever made in my life," he added.
Ghotbi said that he hoped the Reds continue their success,
"I hope they are successful in the Premier league and the Asian competitions."
After leading the team to the title in the last minute of last season, the second campaign has been more difficult with Persepolis struggling to find consistency.
The Iranian-American coach resigned in the close-season but soon returned and as he headed to Dubai, it looks unlikely that he will change his mind this time.