Both teams were the continent's only remaining sides in the men's competition.
But they both lost in Saturday's quarter-final matches - with Senegal going down 4-2 in extra-time to Mexico and Egypt beaten 3-0 by Japan.
The two teams who represented Africa in the women's tournament, Cameroon and South Africa, failed to qualify for the knock-out stages and did not win a single match.
Nigeria, who claimed Africa's first football gold medal at the 1996 games in Atlanta, won through to the final in Beijing, losing to Lionel Messi's Argentina.
"It is a big disappointment to see two good African teams, being eliminated," Cisse said.
"But I take that primarily as proof of a need to continue to work and a need for us to close the gap between African football and football from the other continents."
Senegal, with their inventive play up front, had a decent chance of winning the game but they were badly let down by poor defending overall, especially from Abdoulaye Ba and Papa Gueye.
Gueye was dispossessed after a lazy backpass, with Giovani Dos Santos pouncing on the loose ball to curl in his third goal past goalkeeper Ousmane Mane.
Senegal captain Ba then tried to head the ball back to Mane, only for substitute Raul Jimenez to run on to the loose ball and force the keeper into a save, with Hector Herrera heading in the rebound.
"It is true that certain errors, by certain individuals, cost us the game" Cisse said.
"But please remember that these are young players and they will learn from their mistakes.
"I do not think that we should be too hard on them.
"We were in a very difficult match but we were in a match that we could have also won."
Senegal clawed their way back into the game with second-half goals from Moussa Konate and substitute Ibrahima Balde erasing Mexico's 2-0 lead.
But their errors in extra-time cost them a place in the semi-final.
"We tried to make adjustments to the way we were playing at half-time but what can you do when individual errors are made?" Cisse said.
"That can always bring you down. I was a defender myself and I am well aware of the need for good communication in defence."
"Of the four goals [that Mexico scored] we gave three of them away, so what else can I say, other than we have to keep on working to eliminate errors of this kind, so that we do not repeat them in the future.
"When I think back to the four games that we have played in this tournament, it has been a truly interesting experience for all of us, at our first participation at the Olympic Games."