Ismaili announced on Wednesday that Wotte was due to sign a contract with them, but has suddenly backed down on the move.
While the Dervishes have stated no solid reasons for Wotte's decision, Southampton have announced that he has been reinstalled as manager.
"I am very happy to stay to help this club towards a better future," said Wotte.
"I didn't want to leave while we are in such a difficult situation and I want to stick with the players and the staff at this great club and continue our preparations for life in League One."
Wotte was set to be replaced by another manager as Soton were on the verge of being sold to Pinnacle group, he therefore agreed to take charge of Ismaili.
However, the buyout deal fell through and the Saints' board decided to re-appoint the 48-year-old tactician.
Meanwhile, Ismaili are in search of a new foreign manager ahead of the new season.