The Black Stars — third in Group E going into the match in Kampala — needed a win to keep their hopes alive of making the finals in Russia.
But they had a stoppage time goal disallowed just before the final whistle.
The Ghana Football Association said it had written to FIFA about the performance of South African referee Daniel Bennett and his assistants, Eldrick Adelaide and Steve Marie, both of the Seychelles.
“The GFA filed the protest to football’s world governing body, FIFA, immediately after the match at the Mandela National Stadium in Kampala,” it said in a statement.
“Mr Bennett and (his) assistants denied Ghana a perfect goal in the 93rd minute with television replays showing that it was a perfect goal.”
Ghana had been denied a penalty earlier in the half while several other decisions raised questions about the officials, it added.
“The GFA respectfully asked FIFA to consider the possibility of a replay in order to serve the ends of justice without fear or favour,” the statement added.