The People's Elephant lost their last group fixture 3-0 to Congo outfit .
A victory at home was needed to keep Enyimba's hope of progressing to the knockout stage and as early as the seventh minute Ibrahim Mustapha put the hosts ahead at the Adokiye Amiesimaka Stadium in Port Harcourt.
Williamsville also created chances, Folorunsho Olatunji going close with a header for the Ivorians as they went into the first half break just one goal behind.
The game ended 1-0 as Enyimba could not extend their lead and Williamsville could not equalize.
The Aba based side were are drawn alongside Willamsville of Ivory Coast, Cara Brazzaville of Congo and Malian side Djoliba in group C of the CAF Confederation Cup.
The result means that the Peoples Elephant now have six points from their first three games, with two wins and one loss.
A repeat of the points in the second leg will see Enyimba amass a total of 12 points which should be enough to progress from the group phase.
Enyimba's group stage fixtures
Away vs Williamsville Sunday, July 29
Away vs Djoliba Sunday, August 17
At home vs Cara Brazzaville, Wednesday, August 29.