This comes as Interpol issued a red notice, the closest instrument to an worldwide arrest warrant, on four North Koreans wanted in connection with the murder.
Zahid said the authorities had traveled overseas to an undisclosed country to collect the DNA sample.
The Malaysian authorities have charged an Indonesian woman and a Vietnamese woman with the murder, and are looking for seven North Koreans to question over the case.
He also said 50 North Koreans will be deported from Malaysia for overstaying their visas, despite a ban on North Koreans leaving the country.
"The DNA was taken and brought to Malaysia and matching was made and we confirmed that the body belonged to Kim Jong- Nam". One is of Vietnam national and the other is from Indonesia.
Malaysia has invited Kim Jong-nam's family to claim his body in the next two to three weeks. "If North Korea can not find a neutral venue, we will find one for them".
He said any decision will be subject to negotiations between the two countries amid a diplomatic standoff over the killing.
In a separate development, Prime Minister Najib Razak said Malaysia has not started formal negotiations with North Korea over the release of nine Malaysians stranded in Pyongyang.
However, Malaysian Deputy Police Chief Noor Rashid Ibrahim said yesterday the family had given consent for Malaysia to manage Kim Jong-nam's remains.
Police say the other three, including a North Korean diplomat and an employee of Air Koryo, North Korea's state airline, are believed to be in the North Korean Embassy in Kuala Lumpur.
Deputy Prime Minister Ahmad Zahid Hamidi confirmed on Wednesday that Mr Kim Jong Nam's body had been identified based on DNA samples provided by a child of the deceased. We can not just simply make a decision. That includes a period where the United States has provided $1.35billion (£1.1bn) in assistance to North Korea as an encouragement to take a different pathway.
A giant mosaic created by 10,000 North Koreans holding cards at the May Day stadium in Pyongyang, North Korea.