A casket bearing Woolmer's embalmed body arrived at the Cape Town International Airport shortly before 10:00 am (0800 GMT) on a South African Airways Flight from London.
An AFP photographer saw a wooden box wrapped in plastic sheeting being offloaded from Boeing 747 on the apron and taken with a police escort to the cargo section of the airport. From there it was collected by a van from the Doves funeral group.
Doves Western Cape general manager Theo Rix confirmed the box contained Woolmer's remains.
The body would be kept at a mortuary while his family makes funeral arrangements.
"We are meeting the family tomorrow morning to make the final arrangements," Rix told AFP.
Woolmer's widow, Gill, who lives in Cape Town's Pinelands neighbourhood, has previously said her English-born husband's cremation ceremony would be a private family affair.
A public memorial service for the former South African coach was held in the city earlier this month.
Woolmer, 58, was found dead in his Kingston hotel room on March 18, the day after Pakistan crashed out of the cricket World Cup in an upset loss to Ireland.
His body was held in legal limbo for weeks after an autopsy indicated the former England Test player had been strangled, but investigators have yet to make any arrests.
The Kingston coroner in charge of the case ruled that Woolmer's body could not be released until after an inquest that had been scheduled to begin on April 23 was completed.
But the inquest was cancelled following concerns of a lack of police resources as a Cricket World Cup semi-final game was to be played the following day, police said.
Woolmer's body was then ordered to be released to his family.
His death led to a fevered round of speculation as to the motive for the murder. The most common theory is that his killing was linked to match-fixing and illegal betting in cricket.
Some 30 police investigators are working full-time on the Woolmer case and more than 100 witness statements have been taken.