But Bouka Moutou restored parity for the visitors with just three minutes to end the game silencing the 80,000 fans in the stadium.
But the Egyptians' World Cup hoodoo ended as Salah held his nerve late on to convert the spot kick.
Mohammed Salah shot the home side into the lead in the 63 minute when he beat the offside trap to nutmeg the Congo goalie for the opener.
Egypt has qualified directly for World Cup.
Egypt, though a powerful force in African soccer, have been missing in World Cup tournaments since 1990.
Egypt's coach Hector Cuper has revealed he is ready to face Congo in a major decider despite increasing pressure from nationals for him to prove his worth.
"I am taking hypertension medicine due to the stress I suffer from continuing criticism", he told reporters without specifying who his critics were.
"Life is full of stress, but the challenge of reaching the World Cup is the toughest stress I have faced". It doesn't need the result from its match against Ghana.
Their last group fixture is an inconsequential game away to Ghana while Congo will entertain Uganda.
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