A requiem mass is expected to take place later on Saturday in the athlete's home town of Nyahururu, to the north of Nairobi in Kenya's Rift Valley, followed by the burial at a farm belonging to the family outside town.
The marathon runner died on May 16 at the age of 24, three years after making history at the 2008 Beijing Olympics, when he fell from the balcony of his home after his wife caught him with another woman.
A magistrate at Nakuru High Court, Anyara Emukule, who on May 19 had ruled that the burial should be delayed to allow for an autopsy, said on Friday evening that "everything that needed to be done on the remains, including a post mortem, has already been completed".
Further "postponement of the burial would exacerbate feelings of animosity and mistrust in the family," he ruled.
But he ordered further investigations into the cause of the athlete's death by a new team of investigators based in the capital Nairobi.
The athlete's mother, Hannah Wanjiru, who filed the suit resulting in the initial May 19 postponement of the burial, threatened to take non-legal measures to prevent the burial going ahead.
"I will do everything possible within my powers to stop the burial of my son, proper investigations have not been carried out. How can the burial be held?" Hannah Wanjiru said after the ruling.
Hannah Wanjiru contends that her daughter-in-law Trizah Njeri and the couple's night guard killed her son and then made the incident look like an accidental fall.
The local police have since the beginning of the case stuck to the theory of an accidental fall but two out of the three pathologists who examined the body said the injuries sustained were not consistent with that theory.
Wanjiru made history at the 2008 Beijing Olympics when his winning time of two hours six minutes 32 seconds destroyed the 24-year-old Olympic record of 2:09:21 set in 1984 by Carlos Lopes of Portugal.
It gave Kenya its first Olympic marathon gold.
After Beijing, Wanjiru won the London marathon in 2009 and Chicago in 2009 and 2010.