The Western Province player was felicitated with three other awards by the United Cricket Board of South Africa (UCBSA) at an awards ceremony in Johannesburg on Thursday night.
Besides Cricketer of the Year, Kallis bagged the Players' Player Award, the country's cricket supporters' award, and the Player of the Year award.
Veteran cricketer Gary Kirsten, who retired from all international cricket after the recent New Zealand tour, also received an award for his contributions to the game.
Fast bowler Makhaya Ntini was named South Africa's Player of the Year in the One-day version while all-rounder Lance Klusener became the Player of the Year in the provincial four-day tournament.
Felicitating Kallis, UCB CEO Gerald Majola said, "Jacques is without doubt one of our finest ever cricketers. His performances in the last year have been phenomenal and put him among the game's current greats. These awards show not only what a fine year he has had, but also how well respected he is by his fellow players and by fans."