North Korea had requested the body, but has not confirmed its identity.
It was released as part of a deal under which nine Malaysians previously prevented from leaving North Korea have now arrived home.
The two countries had been locked in a diplomatic row in the wake of the killing in Kuala Lumpur last month.
Both countries had banned each other's citizens from leaving.
Three North Koreans have been allowed to leave Malaysia, Malaysia's chief of police said.
"The body of the DPRK citizen who died in Malaysia and relevant DPRK citizens have returned to the DPRK today via Beijing," Chinese foreign ministry spokesman Lu Kang said during a regular press briefing, using the country's official name, the Democratic People's Republic of Korea.
North Korea is widely suspected to have orchestrated Mr Kim's murder with a nerve agent in Kuala Lumpur's airport.
The late Kim Jong-il's eldest son was passed over for the leadership and was living outside North Korea at the time of his death.
The nine Malaysian nationals were met by their relatives and a large media contingent at Kuala Lumpur airport early on Friday.
Those who have returned include the country's counsellor to North Korea, Mohd Nor Azrin Md Zain, embassy staff, and their families.
They were flown home in a business jet plane piloted by members of the Malaysian air force.
What was the spat about?
Following Mr Kim's killing on 13 February, North Korean officials demanded that the body be handed to them immediately without an autopsy.
Pyongyang reacted angrily when Malaysia refused their requests.
Malaysian authorities said they had the right to conduct an autopsy as he had been killed on Malaysian soil, and said they would only release the body to Mr Kim's family.
This prompted a war of words where North Korea's ambassador Kang Chol accused Malaysia of colluding with "hostile forces", allegations which Kuala Lumpur dubbed as "delusions, lies and half-truths".
Kang Chol was expelled and the Malaysian ambassador to North Korea was also recalled.
Pyongyang then said it would ban all Malaysians in North Korea from leaving until the "situation was resolved", which Malaysia's Prime Minister Najib Razak called an "abhorrent act" that effectively held his citizens hostage.
Kuala Lumpur enacted a tit-for-tat exit ban on North Koreans.
How was it resolved?
Malaysian officials have not hesitated in branding the return of their citizens as a triumph of diplomatic deal-making.
On Friday morning Malaysian Foreign Minister Anifah Aman told reporters: "There can be no substitute for diplomacy, for level-headedness in dealing with such situations, and this has served Malaysia well in this instance."
But the exact circumstances of how the deal was struck remain unclear.
Mr Najib had said earlier that, after challenging negotiations, all North Koreans would be allowed to leave Malaysia - which probably includes those wanted by Malaysian police for questioning.
Japanese news agency Kyodo said two men resembling two wanted North Koreans were seen on a Beijing-bound flight transporting Mr Kim's body on Friday.
The men are thought to be Hyon Kwang Song, the second secretary at the North Korean embassy in Kuala Lumpur, and Kim Uk Il, an employee of North Korea's state airline Air Koryo.
The two men were previously reported to have been holed up in the embassy and refused to take part in investigations.
What's happened to the body?
Mr Kim's body was released to North Korea and flown first to Beijing, and then on to Pyongyang.
Malaysia had previously said it would not release the body until a request came from family members.
On Thursday, Mr Najib said a formal request had been received from the family, but did not give further details. It is not known who exactly requested the body.
Mr Kim's own family previously lived in Macau but they are now thought to be in hiding.
His son Kim Han-sol appeared in a video earlier this month confirming he was with his mother and sister at an unspecified location.