The seven-time African champions are dominating the proceedings and had the match in their pockets when Mohamed Nagy Gedo and Ahmed Ali bagged goals in quickfire succession inside the opening 10 minutes at Ismailia stadium.
Al-Sayed Hamdi made the Burundi keeper pay for his fatal mistakes, scoring the third in the 80thminute to maintain Egypts perfect run in the group stage.
Egypt coach Hassan Shehata reshuffled his squad as he kept some of his key players on the bench like inspirational playmaker Mohamed Abou-Treika, flamboyant winger Mahmoud Abdel-Razek Shikabala, strikers Al-Sayed Hamdi and Ahmed Belal, in addition to his keeper Abdel-Wahed Al-Sayed.
It took only 46 seconds for Gedo to break the deadlock as he picked Ahmed Alis rejected ball and sent it back into the empty net.
Ali then claimed his own piece of the limelight as he headed past the keeper, in the 10thminute, converting an excellent cross from Hossam Ghaly.
He could have doubled his tally but he blasted the ball over the bar from the six yards midway through the first half.
Two goals down, the visitors had a mountain to climb against a vastly experienced side. They tried to react but nothing that could have worried keeper Mohamed Sobhy.
The Pharaohs lost their pace after the break and despite Shehata bringing in all his master pieces with the likes of Abou-Treika, Shikabala, Hosni Abderabou, Walid Soliman and Al-Sayed Hamdi, the team failed to improve.
10 minutes from time, Hamdi scored his teams third, heading in a fine cross from Ahmed Fathi to move to the top of the tournament scorers chart with three goals.
The hosts will now play Kenya on Friday while second-placed Uganda will face DR Congo in the semi-finals.
Watch the Goals: Egypt 3-0 Burundi
First Half Goals
2nd Half