Early goals from Geddo and Ahmed Ali paved way for an expected win as Al-Sayed Hamdi came off the bench to add a third near the end.
The hosts secure top spot in Group A with nine points, five ahead of Uganda who finished second after holding Tanzania to a 1-1 draw earlier.
The result will see Egypt meet Group B runner-up Kenya as leaders DR Congo face Uganda after edging Sudan 2-1.
Early domination…and nothing more
Egypt coach Hassan Shehata handed starts to five Ismaili players before their own fans at Ismailia Stadium, including goalkeeper Mohamed Sobhi who replaced Abdul-Wahed Al-Sayed between the posts.
Ahmed Samir Farag kept his place on the left flank as Amr Al-Sulaya, Abdullah Saied and Ali completed the Dervishes quintet.
Egypt needed no more than one minute to take the lead through Geddo, who scored what could be the easiest goal of his career.
The Ahli striker hit an empty net from point-blank range after Ali’s effort came off the bar, following some shambolic goalkeeping from the Burundi number one.
Ten minutes later, it was two when Ali rose above the poor Burundi keeper to head home Hossam Ghaly’s precise cross for his second of the tournament.
Complacency ruled afterwards as the African champions hardly tried to go for a rout against their hapless opposition.
Ali missed a sitter from six yards midway through the first half after yet another gaffe from the keeper, who was fortunate not to receive more shots on target until the end of the half.
Shehata made several changes at half time, bringing in some high-profile names including Mohamed Abou-Treika , Hosni Abd-Rabou and Shikabala.
But the dull affair went on as the Egypt tactician seemed to be more focused on helping his players gain international match-practice rather than going for a comprehensive scoreline.
Substitute Hamdi put the game to bed with ten minutes to go, heading home Ahmed Fathi’s pinpoint cross to become the competition’s top scorer with three goals in as many games.