He was 77.
He also announced that the new ruler would be proclaimed before the burial at 2pm today.
Ghani, who was in Chennai earlier as part of Prime Minister Datuk Seri Najib Razak’s entourage to India, had returned home on a special flight.
The body of Sultan Iskandar was transported from Puteri Specialist Hospital to Istana Besar at 11.15pm.
It was accompanied by members of the Johor royalty, state exco members and state religious department officers.
The ambulance was escorted by police and Johor Military Force personnel to Istana Besar for final rites.
Those wishing to pay their last respects will have to adhere to the respective dress codes.
Sultan Iskandar will be buried at the Mahmoodiah Royal Mausoleum at 2pm.
The menteri besar also announced a seven-day mourning period for the people of Johor and 40 days for the royal family.
The national and state flags will also be lowered to half mast for a period of seven days.
Sultan Iskandar was admitted to Johor Specialist Hospital late on Thursday for an unspecified illness.
He had undergone a coronary bypass operation in the United States in 2000 and had a bout of bronchitis in January 2008, which saw him being admitted and treated at the hospital.
Earlier in the day, the head of the Johor Council of the Royal Court, Tunku Osman Tunku Temenggong Ahmad, announced the appointment of Tunku Mahkota of Johor Tunku Ibrahim Ismail as the regent.
“The Council of the Royal Court hereby decided under Clause 9(1)(b) and 9(2) First Section of the Johor State Constitution 1895, after receiving the medical report from three medical specialists, to appoint Duli Yang Amat Mulia Tunku Ibrahim Ismail ibni Sultan Iskandar,Tunku Mahkota Johor, as the regent to carry out the duty of the ruler during the illness of Duli Yang Maha Mulia Sultan Iskandar,” he had said at Istana Besar.
The brief solemn ceremony was held at the banquet hall of Istana Besar at 5.15pm.
Also present were State Legislative assembly Speaker Datuk Mohd Ali Hassan and state executive council members.
This is not the first time Tunku Ibrahim was appointed regent.
He was first appointed to the post on April 25, 1984 when Sultan Iskandar was appointed the eighth Yang di- Pertuan Agong.
He was installed as the Tunku Mahkota of Johor on July 3, 1981 at
the age of 22.
Tunku Ibrahim is married to Raja Zarith Sofiah Almarhum Sultan Idris Shah and they have five sons and two daughters.