Shoko’s late strike ensured second place in Group A for the Zimbabwean team, who will now meet Coton Sport of Cameroon in next month’s semi-finals.
Dynamos, beaten finalists in the same competition a decade ago, effectively needed only a draw to ensure their progress but Zamalek had to win away from home to stand any chance of reaching the last four.
The result rendered academic the last Group A match in Cairo between Al Ahli and ASEC Abidjan later on Sunday.
Al Ahli, who had already secured top place in Group A, meet Enyimba of Nigeria in the other semi-final.
The first legs of the semi-finals will be played on the weekend of October 3-5 with the return game two weeks later.