The linesman's flag denied the Black Stars a late victor in the 93rd minute after Raphael Dwamena hit the back of the Ugandan net from a rebound off the goalkeeper.
Ghana, who reached the quarter-finals of the 2010 World Cup in South Africa, are now relying on results going their way if they are to book their ticket to Russian Federation.
According to the GFA, the center referee Daniel Bennet and his assistants Eldrick Adelaide and Steve Marie denied Ghana a flawless goal in the 93rd minute, with television replays showing that it was a ideal goal.
The four time African champions had nearly a new team for the game after the likes Captain Asamoah Gyan, Jonathan Mensah, Harrison Afful, Christian Atsu, Thomas Agyepong, John Boye and Afriyie Acquah all pulled out through injury while the Ayew brothers were not considered.
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"Referee Daniel Bennett just told the Ghana team why he disallowed the goal".
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For Ghana, a win will see them leapfrog Uganda in second with 8 points but their chances will depend on Egypt losing to Congo Brazzaville in Alexandria.
A statement from the Ghana FA read: "The GFA filed the protest to Federation Internationale de Football Association, immediately after the match at the Mandela National Stadium in Kampala".
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"Mr Bennett and assistants denied Ghana a ideal goal in the 93rd minute with television replays showing that it was a flawless goal".
Because apart from this decision, he also made some very contentious decisions like not awarding a penalty to Ghana after winger, Frank Acheampong was shoved off the ball in the Ugandan goal area.
By Saturday's match result, the Black Stars are all but out of the race to Russian Federation 2018 as Egypt will secure the sole Group E ticket should the Pharaohs account for bottom-placed Congo on Sunday.
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