Rules for classification: 1st points; 2nd overall wins; 3rd goal difference; 4th goals scored DGChampionship was decided in a decision game. 1Alma-Ata declared their withdrawal from the league in December 2008. As a consequence, Atyrau were spared from relegation. Subsequently, Alma-Ata and Megasport officials announced that the two clubs have merged to a new team called "Lokomotiv" and expressed their will to move to Astana. Lokomotiv also inherited Alma-Ata's UEFA Europa League 2009–10 spot earned through Kazakhstan Cup 2008. However, Lokomotiv were eventually denied the UEFA License for competing in Europa League due to legal difficulties when creating the new club. Thereby, the potential candidates for one spot left in Europa League were Kaisar, Zhetysu, Shakhter and Okzhetpes. Kaisar and Shakhter were, however, denied a license and Zhetysu eventually withdrew from Europe due to financial difficulties. That left Okzhetpes as the third Europa League participant from Kazakhstan. 2On 2 October 2008, the FFK revisited their decisions upon Shakhter and Vostok for playing a fixed match from 16 September 2008. Shakhter were docked nine points while Vostok were immediately expelled from the competition. The result of the game in question has been cancelled and all remaining Vostok games were counted as won by 3–0 for their opponents. The expulsion of Vostok from Kazakhstan Cup 2008 has been revoked. 3Kairat were docked three points for not paying back existing debts in a timely manner. 4On 20 January 2009, Kairat handed a letter to the FFK citing they will voluntarily withdraw from the Kazakhstan Premier League due to financial reasons. They are eligible for competing in the First Division. 5Astana were docked three points for not paying transfer money to Okzhetpes and Alma-Ata, and for not paying salary to former manager Aleksandr Irkhin. On 20 January 2009, Astana withdrew from 2009 season due to unpaid debts. They do not compete on a professional level, but keep their youth academy. 6On 16 November 2008 FFK board decided not to change the competition format for the 2009 season, what meant that it would feature the same number of teams (16). Since there were four teams originally scheduled to be relegated at the end of the season, the board decided to save from relegation Esil Bogatyr (due to higher amount of points) and Vostok (due to importance of the team for the development of football in the East region of Kazakhstan). However, after two withdrawals the 2009 season features 14 teams. (C) = Champion; (R) = Relegated; (P) = Promoted; (E) = Eliminated; (O) = Play-off winner; (A) = Advances to a further round.
Only applicable when the season is not finished: (Q) = Qualified to the phase of tournament indicated; (TQ) = Qualified to tournament, but not yet to the particular phase indicated; (RQ) = Qualified to the relegation tournament indicated; (DQ) = Disqualified from tournament.