The veteran all-rounder will miss June's tournament in England for undisclosed personal reasons.
Coach Gary Kirsten said South Africa were losing a major asset, describing Kallis as two players in one, but it also means youthful squad can look forward to the one-day tournament without any bitter reminders of past failures.
Kallis was a senior player as South Africa under-performed in a succession of one-day tournaments to earn the team a reputation as 'chokers' in limited-overs competition.
The 37-year-old is the last of the players associated with the bitter disappointments at the last four World Cups in which South Africa have contrived to throw away advantageous situations and crash out of the tournament, sometimes in farcical circumstances.
The Champions Trophy allows a fresh start although the past failures still rankle, particularly as they are continually compared with South Africa's status as the top test-playing nation.
"At some point, we have to cross over that line but you guys could do us a favour and take the pressure off by not talking so much about it," Kirsten told reporters at the team announcement.
South Africa have worked hard at overhauling their one-day side since a surprise loss to New Zealand in the 2011 World Cup quarter-finals.
AB de Villiers has been appointed captain and many players given international exposure to broaden the selection base.
Kallis has not played an ODI in more than a year but was expected to return after participating in the Indian Premier League.
"He's been a great ambassador for the country but if he feels he's not up to the tournament then we have to respect that," added Kirsten.
Kallis was the subject of frequent derision in South Africa throughout his 321-game one-day international career, perceived by a critical public of playing at his own pace more than in the interests of the team.
It has only been in recent years that the value of his record-breaking contribution was more widely appreciated and he has earned grudging respect.
- Sports & Recreation
- South Africa
- Gary Kirsten