Kuwait were banned by the world governing body in October over government interference in domestic football.
FIFA told the KFA the game was to be cancelled unless the ban was lifted by March 10, a KFA official said.
"The time has passed and we haven't been notified by FIFA that the ban is lifted, so we decided to see the game as cancelled for now," said the official.
It was unclear how the match's points were to be awarded or what part Kuwait might play in the rest of the qualifying phase.
Kuwait are due to play their penultimate qualifier at home to Laos on March 24.
FIFA were unavailable for comment.
The KFA had contacted Southeast Asian teams, including Thailand, to try to set up a friendly in place of the qualifier, the official added.
South Korea, who next play Lebanon at home on March 24, lead Group G in Asian qualifying on 18 points.
Kuwait are second on 10 points, ahead of third-placed Lebanon on goal difference.
(Reporting by Hooyeon Kim; Editing by Ian Ransom)
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