Egypt has a golden opportunity to qualify for the 2018 World Cup finals in Russian Federation, the first time since the 1990 World Cup in Italy.
The Ghana federation says it wants FIFA to "examine" the performances of Bennett and his assistant referees in its match.
The atmosphere in Ghana now is a tensed one as many football-loving Ghanaians are feeling a sense of loss and disappointment over Ghana's failed chance at qualifying for the 2018 World Cup in Russian Federation.
As Ghanaians struggle to comprehend referee Bennett's decision, a popular sports journalist, Saddick Adams, commonly referrednto as Sports Obama, is claiming that the goal was disallowed because the time was up.
"Referee Daniel Bennett just told the Ghana team why he disallowed the goal".
Black Stars coach Kwesi Appiah has bestowed the armband on the Foxes star after injuries to regular skipper Asamoah Gyan and Christian Atsu, who had originally been lined up to deputise.More news: ICE: California's 'Sanctuary State' Law Will Force 'At-Large' Arrests
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.
Cranes have to pray that Egypt draws or is beaten by Congo Brazzaville to keep their dreams alive.
The result left Ghana third in their four-team African qualifying group with six points from their five matches.
The GFA says it filed the protest with Federation Internationale de Football Association immediately after the 0-0 draw in Kampala. Despite showing a great performance during the game, Ghana players were not able to score a single goal.
Ghana had been denied a penalty earlier in the half while several other decisions raised questions about the officials, it added.