The Libyan players wore a new white jersey with the three colors of the pre-Gadhafi flag used by the rebels.
Most of Libya’s players were from Benghazi, which fell to the rebels early in the uprising that began in February.
The win gives Libya six points and second place in its group after Zambia.
The game was moved to Egypt because of the fighting in Libya, and was played without an audience in the stadium because of security concerns.
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