Mohamed Salah scored the only goal of the game as Egypt overtook Uganda into top spot in Group E of Africa's World Cup qualifying programme after defeating the Cranes in Alexandria on Tuesday.
The East Africans ran out surprise 1-0 winners when the two sides met in Namboole on Thursday, but the Pharaohs avenged that defeat after Salah's early strike went unanswered.
The win takes Egypt back up to top spot on nine points, two ahead of Uganda in second. Ghana - who travel to Kampala in October - are four points off the pace in third, while Congo-Brazzaville were eliminated earlier on Tuesday after being thrashed 5-1 by the Black Stars.
Egypt took maximum points from their opening two fixtures in the group, but despite beating Uganda en route to second place in the Africa Cup of Nations in Gabon earlier this year, they were found no way past a disciplined Cranes side last week.
Perhaps buoyed into a false sense of security by that victory, Moses Basena's side looked to assert themselves early on in Alexandria, but this approach backfired when Salah was afforded too much space in the sixth-placed
The forward was played in by Abdallah Said and finished from close range past Denis Onyango after the Cranes skipper had blocked the in-form Liverpool hitman's first effort, only to deflect the ball back into his path.
Remarkably, that was the first time the Ugandan backline had been breached during the ongoing qualifying campaign, but the outstanding Onyango ensured that it was to be a one off, making a series of excellent saves to deny Salah and Ahmed Hassan late on.
Egypt could confirm their attendance at a first World Cup since 1990 with a win against Congo in Alexandria on October 8 if Uganda fail to beat Ghana at home.