Irish international Stokes and ex-Kilmarnock and Motherwell forward Lee Erwin both signed for Tractor Club in the summer, but the pair left earlier this month.
Stokes cited family problems and Erwin insisted he was homesick, but that severely irked the Iranians, who reported the pair to FIFA.
However, the 30-year-old has performed a U-turn and has decided to return to Tractor Sazi, according to Scottish Sun.
And he insisted he will fulfill his contract there.
Stokes said: "I had a very good meeting with the team coach, Mohammad Taghavi and he now has a very good understanding of my situation.
"Unfortunately, I had major family problems this month which meant I had to return home," he added.
"During my first spell at the club, these problems meant I couldn't concentrate fully on my football and I could not concentrate. Hopefully, the fans will give me a good reception too," Stokes concluded.