It was largely a lacklustre encounter, however, with seven yellow cards shown and little to enthuse about but for the goals.
The win means that Sudan are all but out of the tournament, unless they can record a big win over Cameroon on January 30, having lost their opening game 3-0 to Zambia, while Egypt have a perfect record of two wins from two.
Desert Hawks striker Hatham Tambal had the first effort on goal, but his shot to the near post was saved by goalkeeper Essam al-Hadary.
Egyptian wonderkid Mohamed Zidan was sent clear on the 10-minute mark, but good cover defending from Ahmed Gibril meant he couldn’t get a shot away.
The breakthrough came on 27 minutes, however, when Hosny Abd Rabou got lucky with the bounce of the ball and found himself one-on-one with Sudanese keeper Mahjoub El Moez, who dived at his feet and brought him down.
Hosny picked himself up and converted from the spot, but for the second time in two matches, was ordered to retake by the referee after it appeared he had not placed it perfectly on the spot.
However, the Egyptian had no trouble in burying the ball at the second attempt.
Sayed Moawad might have doubled the lead early in the second half, but his excellent run and shot was saved by El Moez. And the goalkeeper did brilliantly to keep out a Zidan effort soon afterwards and the game ebbed from end to end, but with little goal-mouth action.
Egypt finally clinched the game 15 minutes from time when good play down the right from The Pharoahs saw Amr Zaki set up Mohamed Aboutraika, who finished at the second attempt.
And Aboutraika made it 3-0 on 82 minutes when he found space on the left and beat the keeper at the near post after faking to cross.
Egypt 3 (Hosny 29pen Aboutraika 78, 82)
Yellow cards: Mahmoud Fathallah, Amr Zaki, Mohamed Aboutraika; Mahjoub El Moez, Mohamed Ali Khider, Alaeldin Ahmed Gibril, Saifeldin Farah
Egypt: 1 Essam al-Hadary, 2 Mahmoud Fathallah (Ahmed Hassan 57), 14 Sayed Moawad, 20 Wael Gomaa, 6 Hani Saied, 7 Ahmed Fathi, 8 Hosny Abd Rabou, 11 Mohamed Shawky, 9 Mohamed Zidan (Mohamed Aboutraika 57), 10 Emad Moteab, 19 Amr Zaki (Ahmed El Mohamady 80)
Sudan: 16 Mahjoub El Moez, 3 Musa Al Tayeb, 4 Mohamed Ali Khider, 7 Alaeldin Ahmed Gibril (Saifeldin Farah 46), 15 Amir Damar Koku, 5 Yousef Alaeldin, 6 Ritshard Justin Lado, 8 Haitham Mustafa, 21 Bahaeldin Abdallah, 10 Hatham Tambal (Abdel Hameed Amari 60), 11 Alaeldin Babiker (Faisal Agab Sido 80)