The Barcelona striker opened, and finished, the scoring to surpass Laurent Pokou's record of 14 goals, which he had equalled against Zambia over the weekend to set the new benchmark at 16 goals.
Eto'o came close in the 2nd minute when he hammered a volley over the bar after his first attempt was saved by Elmuiz Abdalla.
In the 26th minute Eto'o scored with a penalty kick after Achille Emana had been pulled back by Alla Yousif Hado and the referee awarded the penalty.
Cameroon made it 2-0 in the 34th minute when Hamouda El Bashir's attempted clearance from Joel Epalle's cross struck his teammate Mohamed Ali Elkhidir on the back and rolled into the goal.
Sudan came close to scoring early in the second half when Hado's shot was saved by Carlos Kameni.
In the 90th minute, Eto'o scored his 16th goal in the tournament history with a shot after receiving a cross from Modeste M'Bami'.
Cameroon: 3 (Samuel Eto’o 26'& 90', M Ali khidir 34' (og))
Yellow Cards: Yousef Alaeldin, Andre Bikey
Cameroon: 1-Idriss Carlos Kameni 5-Timothee Atouba (Bill Tchato 46') 23-Andre Bikey 4-Rigobert Song 10-Achille Emana (Bertin Tomo 57') 14-Joel Epalle (Paul Tchamba 77') 8-Geremi Njitap 7-Modeste MBami 15-Alexandre Song 9-Samuel Eto’o 21-Joseph-Desire Job
Sudan: 21-Bahaeldin Abdallah 4-Mohamed Ali Khider 3-Musa Al Tayeb 15-Amir Damar Koku 2-Omar Bakheit (Mohamed Tahir 54') 19-Ahmed Al Basha 8-Haitham Mustafa 6-Ritshard Justin Lado 5-Yousef Alaeldin 17-Faisal Agab (Alaeldin Babiker 62') 10-Haitham Tambal (Hassan Isaac 77')