Emad Moteab headed home Egypt's crucial second goal five minutes into injury-time to leave both countries with identical records at the top of Group C in the African qualifying tournament.
The two sides will meet again in Sudan on Wednesday to determine who goes through to the World Cup finals in South Africa next summer.
Bougherra, whose previous game was also an international, has not played for Rangers since the 4-1 defeat to Sevilla on September 29.
He missed the 2-1 victory over Celtic with flu five days later and had to sit out another win at St Johnstone after returning late from Algeria's game against Rwanda.
Rangers manager Walter Smith accepted Bougherra's explanation after the former Charlton defender revealed his phone and passport had been stolen in Paris.
But the 27-year-old then suffered a knee injury in training and missed his club's subsequent five matches.
The latest unavoidable delay in returning from international duty, and the effects of another crucial match, will now cast doubt on Bougherra's participation in the Scottish Premier League clash with Kilmarnock at Ibrox on Saturday.