The matchday five fixture at the Mandela National Stadium in Kampala ended in a 0-0 draw, all but ending the Black Stars' hopes of reaching a fourth successive World Cup.
But the game was marred with controversies, not only by the poor pitch, as Raphael Dwamena's injury time goal from a rebound was ruled out for offside, although television replays showed the FC Zurich striker in good position when Richmond Boakye-Yiadom let out a ferocious shot from outside the box.
"The Ghana Football Association (GFA) has lodged a protest with FIFA over the performance of referee Daniel Bennett and his assistants Eldrick Adelaide and Steve Marie during the 2018 World Cup qualifier against Uganda on Saturday," the statement reads.
"The GFA filed the protest to football's world governing body, FIFA, immediately after the match at the Mandela National Stadium in Kampala.
"Mr Bennett and assistants denied Ghana a perfect goal in the 93rd minute with television replays showing that it was a perfect goal.
"The referee also denied Ghana a penalty earlier in the second-half when Ghana midfielder Frank Acheampong was brought down in the box.
"These and several other decisions by the match officials have left the GFA with no option than to ask FIFA to examine their performances.
"The GFA respectfully asked FIFA to consider the possibility of a replay in order to serve the ends of justice without fear or favour."
Apparently, Dwamena's disallowed goal was not the only trouble spot.
In the first half, Daniel Amartey saw his headed goal from a free-kick ruled out for offside, although TV replays suggest the strike should have stood.
Again, Ghana had a penalty shout ignored in the second half when Frank Acheampong was brought down in the box, to the dismay of the away bench.