Merrikh qualified 4-3 on aggregate for the mini-league phase after a dramatic recovery from a three-goal first leg loss last weekend in the last-32 tie.
Substitute Mohamed Abdulrahman scored the fourth Sudanese goal 18 minutes from time with his first touch of the ball.
Defending champions Mamelodi Sundowns came from behind to draw 1-1 with Kampala Capital City Authority in Uganda and advance 3-2 on aggregate.
Geoffrey Sserunkuma scored his fourth goal in as many Champions League matches to give the Ugandans a half-time lead.
Staring elimination on away goals, Sundowns salvaged a draw 10 minutes from time thanks to a shot into the roof of the net from Liberian Anthony Laffor.
Wydad Casablanca of Morocco, who reached the semi-finals last year, edged Mounana of Gabon 5-4 on penalties after losing 1-0 in Libreville.
Hamidou Sinayoko forced a shootout by scoring four minutes into stoppage time, but Zouheir Laaroubi saved the third Gabonese spot-kick.
The other Moroccan challengers, FUS Rabat, defeated Al Ahly Tripoli of Libya 3-1, but were eliminated on away goals.
After Brahim El Bahri bagged a brace to give FUS a two-goal lead by the break, Mouayad Ali halved the deficit three minutes into the second half.
USM Alger of Algeria, the 2015 runners-up, secured a group slot despite playing 65 minutes with 10 men in a 1-0 defeat by Rail Kadiogo in Burkina Faso.
Amir Sayoud, who scored in a 2-0 first leg win by USM, was sent off after two yellow cards and Mohamed Kahan scored the Kadiogo goal on 53 minutes.
Hopes of a Madagascar club reaching the group stage for the first time were dashed when CNaPS Sport were held 1-1 by Coton Sport of Cameroon in Antananarivo.
Coton took a 1-0 first leg lead to the vast Indian Ocean island and doubled their overall advantage when Souleymanou Moussa struck on the hour mark.
Zanaco of Zambia were another team to progress, although they could only draw 0-0 with Young Africans of Tanzania in Lusaka.
The Zambians won on away goals after drawing 1-1 in Dar es Salaam a week ago.
Another nine second legs are scheduled for Sunday.