Kinnear, the minister said, had been "the top of the crop" - and had been ranked the top police investigator in the Western Cape, and number three in South Africa.
Kinnear had been "not just an ordinary human being, but an extraordinary human being".
The family had demanded of him that Kinnear could not become "a statistic". He said "they want to know what happened".
"It is clear we have lost a good man ... Usually, police are lambasted ... who nobody appreciates. By contrast, [the media] was unanimous ... that Kinnear was 'the best of the best'.
"That tells you what kind of man we have lost," Cele said.
He confirmed that other police officers had received threats to their lives, including Major General Andre Lincoln, and would be protected.
Kinnear's killing is suspected to have been an assassination, although this has not been confirmed by police. They would also not speculate about the possible motive for the murder.
Residents in Bishop Lavis told News24 that shots were heard at around 15:00.
In a statement, national police commissioner General Khehla John Sitole said: "We are all saddened by this tragic untimely loss of Colonel Kinnear and his murder is huge loss to South Africa and its people."
Sitole tasked the provincial commissioner of the Western Cape, Lieutenant-General Yolisa Matakata, with immediately activating the 72-Hour Activation Plan.
Kinnear was attached to the Western Cape Anti-Gang Unit as a section commander and was involved in investigations in several high-profile cases, which resulted in multiple arrests.