Kuwait has been suspended by FIFA and unable to play since October because of government interference in how the federation is run.
The ban effectively ended Kuwait's qualifying chance when it still had three games left.
FIFA says its disciplinary panel also reprimanded the Kuwaiti body for forfeiting games at home to Laos and at South Korea in March.
Kuwait had previously failed to play in November against Myanmar which got a 3-0 win by forfeit.
South Korea advanced as group winner to the next stage of qualifying for the 2018 tournament in Russia. The final Asian group stage is drawn next Tuesday in Kuala Lumpur, Malaysia.