Their Group G triumph was followed by a 1-0 home victory for Algeria over Mali as they confirmed their dominance in Group H.
Both Algeria and Egypt had already secured their progression to the final phase of African qualifiers and now await Monday's draw for the play-off matches featuring 10 teams.
A 51st minute strike from El Arabi Soudani ensured victory for Algeria in Blida and 15 points out of a possible 18 in their group.
But their efforts were bettered by the Egyptians despite a comical own goal in the opening four minutes when English-born defender Adam El Abd, on his competitive debut, miscued a clearance and the back spin beat his own goalkeeper.
Captain Hossam Ghaly ensured the early mistake would not set the tone for Egypt's performance as he steered home an equaliser in the 38th minute after Guinea failed to clear a free-kick from Mohamed Aboutrika.
Guinea were reduced to 10 men early in the second half when defender Kamil Zayatte was sent off and Aboutrika converted from the penalty spot.
Guinea, who finished second in Group G and were already out of World Cup contention before Tuesday's match, were not done, however, and equalised just before the hour mark through Seydouba Soumah.
The teams were level heading into the final 10 minutes but goals from Mohamed Salah and Amr Zaki as the clocked ticked down were enough for Egypt to secure a sixth group win.
Egypt and Algeria join Burkina Faso, Cameroon, Cape Verde Islands, Ethiopia, Ivory Coast, Ghana, Nigeria and Senegal in the decisive round of matches over the next two months to decide Africa's representatives in Brazil.