Both polled 86 votes ahead of Australians Glenn McGrath (39), Adam Gilchrist (29) and Ricky Ponting (19).
Kallis also won the Test player of the year award and England's Kevin Pietersen was crowned the one-day player of the year.
Flintoff had 366 runs at 30.5 and claimed 44 wickets at 24.68 at Test level in the voting period from August 1 2004 to July 31 2005, which only included the opening Test of England's recent 2-1 win over Australia in the Ashes series.
During the voting period, Kallis played 15 Tests and was comfortably the most prolific batsman in the world during that time, with 1497 runs at 71.28, including six hundreds, the most by any player, and a total of 14 scores of 50 or more.
He took 20 Test wickets and 16 catches, mainly in the slip cordon.
Kallis was named the Test player of the year well ahead of McGrath and Shane Warne.
The allrounder polled 115 votes to comfortably defeat McGrath (41) and Warne (29).
Pietersen was named the one-day player of the year beating team-mate Andrew Flintoff for the award.
Pietersen, 25, polled 91 votes ahead of Flintoff (52) and Australia's Andrew Symonds (26).
Pietersen also won the emerging player of the year award.
"It's been a whirlwind, the last 12 months. I'm just thrilled to be here, and I thank all the people that have helped me in achieving this success," Pietersen said at the presentation.
During the voting period from August 1, 2004 to July 31, 2005, Pietersen played 21 one-day internationals and scored 786 runs at an average of 87.33 with three hundreds, all against South Africa.
The South African-born right-hander made four other scores of 50 or more and those runs were made with a remarkable strike-rate of 99.49 runs per hundred balls.
Australian Simon Taufel was named Umpire of the Year for the second successive year.
Taufel, 34, was the clear winner of the trophy ahead of Pakistan's Aleem Dar and Rudi Koertzen of South Africa after votes were tallied from the captains of the ten Test-playing countries and the seven members of the Elite Panel of ICC Match Referees.
The England cricket team were named as the recipients of the Spirit of Cricket Award.
The award goes to the team which, in the opinion of the elite panel of umpires and referees and the captains of the ten Test teams, has best conducted itself on the field within the spirit of the game.
The World ODI Team of the Year announced was: Marvan Atapattu (captain, Sri Lanka), Adam Gilchrist (wicketkeeper, Australia), Rahul Dravid (India), Kevin Pietersen (England), Inzamam-ul-Haq (Pakistan), Andrew Flintoff (England), Andrew Symonds (Australia), Daniel Vettori (New Zealand), Brett Lee (Australia), Naved-ul-Hasan (Pakistan), Glenn McGrath (Australia). 12th man: Jacques Kallis (South Africa).