Ferroviario Beira of Mozambique and Zesco United of Zambia qualified for CAF club competition quarter-finals Friday after Sudan were banned from competing internationally.
FIFA suspended the east African nation over government interference after national federation president Mutasim Gaafar Sir Eklkhatim was illegally replaced.
The decision robbed Al Merrikh of a probable Champions League last-eight place and Al Hilal Obeid of an already-secured Confederation Cup quarter-finals spot.
With Merrikh and already eliminated fellow Sudanese side Al Hilal Omdurman banished from Group A, Ferroviario join Etoile Sahel of Tunisia in the Champions League knockout phase.
The elimination of Confederation Cup Group C leaders Hilal Obeid means Zesco not only qualify, but win the mini-league.
Smouha of Egypt, who jumped from fourth to second in the revised standings, will advance with Zesco if they avoid defeat away to Recreativo Libolo of Angola in Calulo Sunday.
Government interference in football is a recurring African problem with Mali barred for several months this year.
The suspension forced Djoliba and Onze Createurs to withdraw from the Confederation Cup after they built first-leg leads in qualifying ties.